Results

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Go to: Gene Set Collection: KEGG
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Go to: Gene Set Collection: Broad.c2.CP.KEGG
Go to: Gene Set Collection: Broad.c2.CP.REACTOME
Go to: Gene Set Collection: Broad.c3.TFT
Go to: Gene Set Collection: Broad.c4.CGN
Go to: Gene Set Collection: Broad.c4.CM
Go to: Gene Set Collection: Broad.c5.BP
Go to: Gene Set Collection: Broad.c5.CC
Go to: Gene Set Collection: Broad.c5.MF
Go to: Gene Set Collection: PMID
Go to: Gene Set Collection: Prosite
Go to: Gene Set Collection: Enzyme
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Go to: Gene Set Collection: ppi.anyDB
Go to: Gene Set Collection: pathwayCommons.cell-map
Go to: Gene Set Collection: pathwayCommons.nci-nature
Go to: Gene Set Collection: pathwayCommons.reactome
Go to: Gene Set Collection: tfbsK3Z3

AFA results for: SAHA.ls

Click on the heading for any column to sort by that column.

Gene Set Collection: KEGG

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
KEGG 03040 View Gene Set 2.252e-11 128 4.82e-09 1 Spliceosome www.genome.jp/d...
KEGG 03018 View Gene Set 7.784e-06 59 0.0008329 2 RNA degradation www.genome.jp/d...
KEGG 04110 View Gene Set 2.745e-05 128 0.001958 3 Cell cycle www.genome.jp/d...
KEGG 03410 View Gene Set 0.0001001 34 0.005353 4 Base excision repair www.genome.jp/d...
KEGG 03030 View Gene Set 0.001159 36 0.04963 5 DNA replication www.genome.jp/d...

Gene Set Collection: GO

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
GO GO:0090304 View Gene Set 1.693e-59 3724 2.261e-55 1 nucleic acid metabolic process amigo.geneontol...
GO GO:0005634 View Gene Set 1.332e-55 5198 8.899e-52 2 nucleus amigo.geneontol...
GO GO:0003676 View Gene Set 1.65e-50 2979 7.349e-47 3 nucleic acid binding amigo.geneontol...
GO GO:0010467 View Gene Set 2.394e-50 3806 7.997e-47 4 gene expression amigo.geneontol...
GO GO:0006139 View Gene Set 4.693e-43 4294 1.254e-39 5 nucleobase nucleoside nucleotide and nucleic acid metabolic process amigo.geneontol...
GO GO:0016070 View Gene Set 3.017e-42 2596 6.719e-39 6 RNA metabolic process amigo.geneontol...
GO GO:0044428 View Gene Set 1.582e-41 1938 3.019e-38 7 nuclear part amigo.geneontol...
GO GO:0044260 View Gene Set 7.711e-39 5699 1.288e-35 8 cellular macromolecule metabolic process amigo.geneontol...
GO GO:0031981 View Gene Set 6.967e-35 1518 1.034e-31 9 nuclear lumen amigo.geneontol...
GO GO:0034645 View Gene Set 1.068e-34 3529 1.426e-31 10 cellular macromolecule biosynthetic process amigo.geneontol...
GO GO:0009059 View Gene Set 1.545e-34 3597 1.854e-31 11 macromolecule biosynthetic process amigo.geneontol...
GO GO:0034641 View Gene Set 1.665e-34 4584 1.854e-31 11 cellular nitrogen compound metabolic process amigo.geneontol...
GO GO:0003723 View Gene Set 4.623e-31 732 4.751e-28 13 RNA binding amigo.geneontol...
GO GO:0006350 View Gene Set 1.28e-30 2744 1.221e-27 14 transcription amigo.geneontol...
GO GO:0043170 View Gene Set 6.749e-30 6274 6.011e-27 15 macromolecule metabolic process amigo.geneontol...
GO GO:0006807 View Gene Set 1.504e-29 4698 1.256e-26 16 nitrogen compound metabolic process amigo.geneontol...
GO GO:0010468 View Gene Set 2.242e-29 2958 1.762e-26 17 regulation of gene expression amigo.geneontol...
GO GO:0010556 View Gene Set 1.13e-28 2901 8.386e-26 18 regulation of macromolecule biosynthetic process amigo.geneontol...
GO GO:0006396 View Gene Set 3.116e-28 578 2.191e-25 19 RNA processing amigo.geneontol...
GO GO:0045449 View Gene Set 3.733e-28 2647 2.494e-25 20 regulation of transcription amigo.geneontol...
GO GO:0070013 View Gene Set 8.004e-28 1845 5.092e-25 21 intracellular organelle lumen amigo.geneontol...
GO GO:0060255 View Gene Set 4.367e-27 3411 2.652e-24 22 regulation of macromolecule metabolic process amigo.geneontol...
GO GO:0043233 View Gene Set 1.09e-26 1881 6.332e-24 23 organelle lumen amigo.geneontol...
GO GO:0005654 View Gene Set 1.372e-26 939 7.639e-24 24 nucleoplasm amigo.geneontol...
GO GO:0031974 View Gene Set 2.062e-25 1917 1.102e-22 25 membrane-enclosed lumen amigo.geneontol...
GO GO:0016071 View Gene Set 2.268e-23 381 1.165e-20 26 mRNA metabolic process amigo.geneontol...
GO GO:0031326 View Gene Set 2.39e-23 3048 1.183e-20 27 regulation of cellular biosynthetic process amigo.geneontol...
GO GO:0003677 View Gene Set 3.054e-23 2028 1.457e-20 28 DNA binding amigo.geneontol...
GO GO:0009889 View Gene Set 4.93e-23 3070 2.271e-20 29 regulation of biosynthetic process amigo.geneontol...
GO GO:0008380 View Gene Set 8.024e-23 300 3.573e-20 30 RNA splicing amigo.geneontol...
GO GO:0006397 View Gene Set 7.505e-22 317 3.234e-19 31 mRNA processing amigo.geneontol...
GO GO:0019219 View Gene Set 7.992e-22 3040 3.337e-19 32 regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process amigo.geneontol...
GO GO:0080090 View Gene Set 2.462e-21 3585 9.968e-19 33 regulation of primary metabolic process amigo.geneontol...
GO GO:0051171 View Gene Set 4.832e-21 3066 1.899e-18 34 regulation of nitrogen compound metabolic process amigo.geneontol...
GO GO:0030529 View Gene Set 2.824e-20 504 1.078e-17 35 ribonucleoprotein complex amigo.geneontol...
GO GO:0044451 View Gene Set 6.591e-19 600 2.446e-16 36 nucleoplasm part amigo.geneontol...
GO GO:0005730 View Gene Set 7.333e-19 734 2.648e-16 37 nucleolus amigo.geneontol...
GO GO:0044249 View Gene Set 5.672e-18 4326 1.994e-15 38 cellular biosynthetic process amigo.geneontol...
GO GO:0005694 View Gene Set 7.578e-18 507 2.596e-15 39 chromosome amigo.geneontol...
GO GO:0006351 View Gene Set 1.184e-17 1949 3.955e-15 40 transcription DNA-dependent amigo.geneontol...
GO GO:0032774 View Gene Set 1.26e-17 1953 4.107e-15 41 RNA biosynthetic process amigo.geneontol...
GO GO:0043227 View Gene Set 3.23e-17 8383 1.027e-14 42 membrane-bounded organelle amigo.geneontol...
GO GO:0043231 View Gene Set 3.601e-17 8376 1.119e-14 43 intracellular membrane-bounded organelle amigo.geneontol...
GO GO:0051252 View Gene Set 1.382e-16 1869 4.195e-14 44 regulation of RNA metabolic process amigo.geneontol...
GO GO:0031323 View Gene Set 2.356e-16 3768 6.994e-14 45 regulation of cellular metabolic process amigo.geneontol...
GO GO:0006355 View Gene Set 1.359e-15 1820 3.886e-13 46 regulation of transcription DNA-dependent amigo.geneontol...
GO GO:0009058 View Gene Set 1.367e-15 4436 3.886e-13 46 biosynthetic process amigo.geneontol...
GO GO:0051276 View Gene Set 2.753e-15 548 7.661e-13 48 chromosome organization amigo.geneontol...
GO GO:0000775 View Gene Set 1.223e-14 146 3.335e-12 49 chromosome centromeric region amigo.geneontol...
GO GO:0019222 View Gene Set 7.331e-14 4060 1.959e-11 50 regulation of metabolic process amigo.geneontol...
GO GO:0043229 View Gene Set 2.186e-13 9346 5.726e-11 51 intracellular organelle amigo.geneontol...
GO GO:0043226 View Gene Set 2.816e-13 9360 7.234e-11 52 organelle amigo.geneontol...
GO GO:0000375 View Gene Set 3.303e-13 106 8.327e-11 53 RNA splicing via transesterification reactions amigo.geneontol...
GO GO:0044427 View Gene Set 4.233e-13 420 1.047e-10 54 chromosomal part amigo.geneontol...
GO GO:0005681 View Gene Set 6.032e-13 135 1.465e-10 55 spliceosomal complex amigo.geneontol...
GO GO:0016568 View Gene Set 1.973e-12 324 4.708e-10 56 chromatin modification amigo.geneontol...
GO GO:0043228 View Gene Set 5.157e-12 2690 1.188e-09 57 non-membrane-bounded organelle amigo.geneontol...
GO GO:0043232 View Gene Set 5.157e-12 2690 1.188e-09 57 intracellular non-membrane-bounded organelle amigo.geneontol...
GO GO:0000279 View Gene Set 6.886e-12 406 1.559e-09 59 M phase amigo.geneontol...
GO GO:0030528 View Gene Set 1.437e-11 950 3.2e-09 60 transcription regulator activity amigo.geneontol...
GO GO:0022403 View Gene Set 2.714e-11 522 5.945e-09 61 cell cycle phase amigo.geneontol...
GO GO:0010629 View Gene Set 3.406e-11 573 7.338e-09 62 negative regulation of gene expression amigo.geneontol...
GO GO:0010605 View Gene Set 3.672e-11 827 7.786e-09 63 negative regulation of macromolecule metabolic process amigo.geneontol...
GO GO:0000793 View Gene Set 3.748e-11 136 7.823e-09 64 condensed chromosome amigo.geneontol...
GO GO:0006259 View Gene Set 3.915e-11 592 8.046e-09 65 DNA metabolic process amigo.geneontol...
GO GO:0000819 View Gene Set 7.061e-11 38 1.429e-08 66 sister chromatid segregation amigo.geneontol...
GO GO:0048285 View Gene Set 7.916e-11 286 1.579e-08 67 organelle fission amigo.geneontol...
GO GO:0000280 View Gene Set 9.148e-11 276 1.771e-08 68 nuclear division amigo.geneontol...
GO GO:0007067 View Gene Set 9.148e-11 276 1.771e-08 68 mitosis amigo.geneontol...
GO GO:0000087 View Gene Set 1.102e-10 286 2.103e-08 70 M phase of mitotic cell cycle amigo.geneontol...
GO GO:0000070 View Gene Set 1.136e-10 37 2.138e-08 71 mitotic sister chromatid segregation amigo.geneontol...
GO GO:0044237 View Gene Set 1.162e-10 7431 2.157e-08 72 cellular metabolic process amigo.geneontol...
GO GO:0000377 View Gene Set 1.225e-10 97 2.211e-08 73 RNA splicing via transesterification reactions with bulged adenosine as nucleophile amigo.geneontol...
GO GO:0000398 View Gene Set 1.225e-10 97 2.211e-08 73 nuclear mRNA splicing via spliceosome amigo.geneontol...
GO GO:0000278 View Gene Set 1.585e-10 489 2.823e-08 75 mitotic cell cycle amigo.geneontol...
GO GO:0006325 View Gene Set 1.731e-10 425 3.042e-08 76 chromatin organization amigo.geneontol...
GO GO:0032991 View Gene Set 2.825e-10 3237 4.901e-08 77 macromolecular complex amigo.geneontol...
GO GO:0016481 View Gene Set 9.853e-10 512 1.688e-07 78 negative regulation of transcription amigo.geneontol...
GO GO:0022613 View Gene Set 1.129e-09 194 1.91e-07 79 ribonucleoprotein complex biogenesis amigo.geneontol...
GO GO:0016604 View Gene Set 1.199e-09 198 2.002e-07 80 nuclear body amigo.geneontol...
GO GO:0044238 View Gene Set 1.56e-09 7629 2.574e-07 81 primary metabolic process amigo.geneontol...
GO GO:0007059 View Gene Set 1.693e-09 94 2.758e-07 82 chromosome segregation amigo.geneontol...
GO GO:0022402 View Gene Set 2.129e-09 676 3.427e-07 83 cell cycle process amigo.geneontol...
GO GO:0009892 View Gene Set 3.55e-09 889 5.646e-07 84 negative regulation of metabolic process amigo.geneontol...
GO GO:0010558 View Gene Set 3.982e-09 611 6.259e-07 85 negative regulation of macromolecule biosynthetic process amigo.geneontol...
GO GO:0008270 View Gene Set 4.663e-09 2009 7.244e-07 86 zinc ion binding amigo.geneontol...
GO GO:0045934 View Gene Set 7.834e-09 574 1.203e-06 87 negative regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process amigo.geneontol...
GO GO:0031324 View Gene Set 1.277e-08 809 1.939e-06 88 negative regulation of cellular metabolic process amigo.geneontol...
GO GO:0051172 View Gene Set 1.423e-08 580 2.136e-06 89 negative regulation of nitrogen compound metabolic process amigo.geneontol...
GO GO:0000776 View Gene Set 1.827e-08 92 2.713e-06 90 kinetochore amigo.geneontol...
GO GO:0008168 View Gene Set 2.165e-08 176 3.178e-06 91 methyltransferase activity amigo.geneontol...
GO GO:0031327 View Gene Set 2.216e-08 629 3.218e-06 92 negative regulation of cellular biosynthetic process amigo.geneontol...
GO GO:0009890 View Gene Set 3.498e-08 642 5.025e-06 93 negative regulation of biosynthetic process amigo.geneontol...
GO GO:0022618 View Gene Set 4.101e-08 76 5.828e-06 94 ribonucleoprotein complex assembly amigo.geneontol...
GO GO:0000123 View Gene Set 4.239e-08 50 5.962e-06 95 histone acetyltransferase complex amigo.geneontol...
GO GO:0016741 View Gene Set 4.861e-08 179 6.764e-06 96 transferase activity transferring one-carbon groups amigo.geneontol...
GO GO:0034470 View Gene Set 8.735e-08 193 1.203e-05 97 ncRNA processing amigo.geneontol...
GO GO:0051253 View Gene Set 1.335e-07 420 1.819e-05 98 negative regulation of RNA metabolic process amigo.geneontol...
GO GO:0000228 View Gene Set 1.478e-07 177 1.995e-05 99 nuclear chromosome amigo.geneontol...
GO GO:0030518 View Gene Set 2.017e-07 73 2.695e-05 100 steroid hormone receptor signaling pathway amigo.geneontol...
GO GO:0045892 View Gene Set 2.242e-07 413 2.965e-05 101 negative regulation of transcription DNA-dependent amigo.geneontol...
GO GO:0003700 View Gene Set 2.686e-07 964 3.518e-05 102 sequence-specific DNA binding transcription factor activity amigo.geneontol...
GO GO:0000779 View Gene Set 2.843e-07 79 3.687e-05 103 condensed chromosome centromeric region amigo.geneontol...
GO GO:0016563 View Gene Set 3.873e-07 430 4.976e-05 104 transcription activator activity amigo.geneontol...
GO GO:0008134 View Gene Set 4.224e-07 525 5.374e-05 105 transcription factor binding amigo.geneontol...
GO GO:0007049 View Gene Set 4.333e-07 1006 5.462e-05 106 cell cycle amigo.geneontol...
GO GO:0006366 View Gene Set 4.703e-07 919 5.872e-05 107 transcription from RNA polymerase II promoter amigo.geneontol...
GO GO:0006974 View Gene Set 5.382e-07 412 6.657e-05 108 response to DNA damage stimulus amigo.geneontol...
GO GO:0006260 View Gene Set 7.84e-07 239 9.609e-05 109 DNA replication amigo.geneontol...
GO GO:0000245 View Gene Set 9.741e-07 34 0.0001183 110 spliceosome assembly amigo.geneontol...
GO GO:0010564 View Gene Set 1.076e-06 161 0.0001295 111 regulation of cell cycle process amigo.geneontol...
GO GO:0034660 View Gene Set 1.146e-06 236 0.0001367 112 ncRNA metabolic process amigo.geneontol...
GO GO:0030522 View Gene Set 1.188e-06 95 0.0001404 113 intracellular receptor mediated signaling pathway amigo.geneontol...
GO GO:0006376 View Gene Set 1.506e-06 15 0.0001764 114 mRNA splice site selection amigo.geneontol...
GO GO:0044446 View Gene Set 1.581e-06 5019 0.0001837 115 intracellular organelle part amigo.geneontol...
GO GO:0006412 View Gene Set 1.935e-06 412 0.0002229 116 translation amigo.geneontol...
GO GO:0000777 View Gene Set 1.975e-06 74 0.0002256 117 condensed chromosome kinetochore amigo.geneontol...
GO GO:0006996 View Gene Set 2.303e-06 1501 0.0002607 118 organelle organization amigo.geneontol...
GO GO:0051427 View Gene Set 2.356e-06 90 0.0002645 119 hormone receptor binding amigo.geneontol...
GO GO:0003712 View Gene Set 2.967e-06 364 0.0003303 120 transcription cofactor activity amigo.geneontol...
GO GO:0003682 View Gene Set 3.005e-06 178 0.0003318 121 chromatin binding amigo.geneontol...
GO GO:0006357 View Gene Set 4.012e-06 760 0.0004393 122 regulation of transcription from RNA polymerase II promoter amigo.geneontol...
GO GO:0035257 View Gene Set 4.218e-06 79 0.0004582 123 nuclear hormone receptor binding amigo.geneontol...
GO GO:0006338 View Gene Set 4.377e-06 59 0.0004716 124 chromatin remodeling amigo.geneontol...
GO GO:0007051 View Gene Set 4.539e-06 57 0.0004851 125 spindle organization amigo.geneontol...
GO GO:0006281 View Gene Set 4.749e-06 309 0.0005035 126 DNA repair amigo.geneontol...
GO GO:0043565 View Gene Set 6.323e-06 638 0.0006652 127 sequence-specific DNA binding amigo.geneontol...
GO GO:0044422 View Gene Set 6.449e-06 5089 0.0006731 128 organelle part amigo.geneontol...
GO GO:0003713 View Gene Set 7.491e-06 215 0.0007758 129 transcription coactivator activity amigo.geneontol...
GO GO:0008152 View Gene Set 8.218e-06 8439 0.0008445 130 metabolic process amigo.geneontol...
GO GO:0016607 View Gene Set 9.134e-06 116 0.0009315 131 nuclear speck amigo.geneontol...
GO GO:0016573 View Gene Set 1.055e-05 56 0.001068 132 histone acetylation amigo.geneontol...
GO GO:0006310 View Gene Set 1.176e-05 130 0.001182 133 DNA recombination amigo.geneontol...
GO GO:0007052 View Gene Set 1.187e-05 22 0.001183 134 mitotic spindle organization amigo.geneontol...
GO GO:0005622 View Gene Set 1.431e-05 11329 0.001414 135 intracellular amigo.geneontol...
GO GO:0003702 View Gene Set 1.439e-05 239 0.001414 135 RNA polymerase II transcription factor activity amigo.geneontol...
GO GO:0006473 View Gene Set 1.552e-05 61 0.001513 137 protein amino acid acetylation amigo.geneontol...
GO GO:0045941 View Gene Set 1.632e-05 599 0.00158 138 positive regulation of transcription amigo.geneontol...
GO GO:0005667 View Gene Set 1.648e-05 201 0.001584 139 transcription factor complex amigo.geneontol...
GO GO:0044424 View Gene Set 1.667e-05 10976 0.00159 140 intracellular part amigo.geneontol...
GO GO:0051301 View Gene Set 1.709e-05 358 0.00162 141 cell division amigo.geneontol...
GO GO:0016564 View Gene Set 2.162e-05 342 0.002034 142 transcription repressor activity amigo.geneontol...
GO GO:0045893 View Gene Set 2.814e-05 516 0.002626 143 positive regulation of transcription DNA-dependent amigo.geneontol...
GO GO:0016585 View Gene Set 2.83e-05 84 0.002626 143 chromatin remodeling complex amigo.geneontol...
GO GO:0043543 View Gene Set 2.856e-05 72 0.002632 145 protein amino acid acylation amigo.geneontol...
GO GO:0000785 View Gene Set 3.188e-05 213 0.002917 146 chromatin amigo.geneontol...
GO GO:0016569 View Gene Set 3.212e-05 165 0.002919 147 covalent chromatin modification amigo.geneontol...
GO GO:0005488 View Gene Set 3.521e-05 12334 0.003179 148 binding amigo.geneontol...
GO GO:0016570 View Gene Set 3.674e-05 162 0.003282 149 histone modification amigo.geneontol...
GO GO:0046914 View Gene Set 3.685e-05 2285 0.003282 149 transition metal ion binding amigo.geneontol...
GO GO:0000122 View Gene Set 3.729e-05 292 0.003283 151 negative regulation of transcription from RNA polymerase II promoter amigo.geneontol...
GO GO:0043189 View Gene Set 3.736e-05 15 0.003283 151 H4/H2A histone acetyltransferase complex amigo.geneontol...
GO GO:0009952 View Gene Set 4.152e-05 155 0.003626 153 anterior/posterior pattern formation amigo.geneontol...
GO GO:0032268 View Gene Set 4.276e-05 576 0.003709 154 regulation of cellular protein metabolic process amigo.geneontol...
GO GO:0030521 View Gene Set 4.39e-05 47 0.003784 155 androgen receptor signaling pathway amigo.geneontol...
GO GO:0051254 View Gene Set 4.524e-05 522 0.003874 156 positive regulation of RNA metabolic process amigo.geneontol...
GO GO:0043967 View Gene Set 4.564e-05 25 0.003884 157 histone H4 acetylation amigo.geneontol...
GO GO:0008757 View Gene Set 4.721e-05 91 0.003992 158 S-adenosylmethionine-dependent methyltransferase activity amigo.geneontol...
GO GO:0070647 View Gene Set 4.826e-05 356 0.004055 159 protein modification by small protein conjugation or removal amigo.geneontol...
GO GO:0005876 View Gene Set 4.876e-05 35 0.004071 160 spindle microtubule amigo.geneontol...
GO GO:0006399 View Gene Set 4.997e-05 118 0.004147 161 tRNA metabolic process amigo.geneontol...
GO GO:0000184 View Gene Set 5.263e-05 30 0.00433 162 nuclear-transcribed mRNA catabolic process nonsense-mediated decay amigo.geneontol...
GO GO:0032446 View Gene Set 5.315e-05 310 0.00433 162 protein modification by small protein conjugation amigo.geneontol...
GO GO:0045815 View Gene Set 5.316e-05 10 0.00433 162 positive regulation of gene expression epigenetic amigo.geneontol...
GO GO:0007346 View Gene Set 5.417e-05 174 0.004364 165 regulation of mitotic cell cycle amigo.geneontol...
GO GO:0010557 View Gene Set 5.423e-05 702 0.004364 165 positive regulation of macromolecule biosynthetic process amigo.geneontol...
GO GO:0030530 View Gene Set 5.603e-05 17 0.004482 167 heterogeneous nuclear ribonucleoprotein complex amigo.geneontol...
GO GO:0032583 View Gene Set 5.721e-05 223 0.00455 168 regulation of gene-specific transcription amigo.geneontol...
GO GO:0006401 View Gene Set 6.199e-05 74 0.004901 169 RNA catabolic process amigo.geneontol...
GO GO:0034621 View Gene Set 6.247e-05 458 0.00491 170 cellular macromolecular complex subunit organization amigo.geneontol...
GO GO:0042254 View Gene Set 7.026e-05 130 0.005489 171 ribosome biogenesis amigo.geneontol...
GO GO:0051246 View Gene Set 8.156e-05 652 0.006335 172 regulation of protein metabolic process amigo.geneontol...
GO GO:0008033 View Gene Set 9.005e-05 78 0.006954 173 tRNA processing amigo.geneontol...
GO GO:0044454 View Gene Set 9.072e-05 139 0.006966 174 nuclear chromosome part amigo.geneontol...
GO GO:0008170 View Gene Set 9.26e-05 58 0.00707 175 N-methyltransferase activity amigo.geneontol...
GO GO:0042809 View Gene Set 9.96e-05 16 0.007561 176 vitamin D receptor binding amigo.geneontol...
GO GO:0000940 View Gene Set 0.0001036 12 0.007822 177 outer kinetochore of condensed chromosome amigo.geneontol...
GO GO:0035267 View Gene Set 0.0001124 14 0.008433 178 NuA4 histone acetyltransferase complex amigo.geneontol...
GO GO:0008139 View Gene Set 0.0001201 9 0.008966 179 nuclear localization sequence binding amigo.geneontol...
GO GO:0006403 View Gene Set 0.0001258 104 0.009266 180 RNA localization amigo.geneontol...
GO GO:0008608 View Gene Set 0.0001262 8 0.009266 180 attachment of spindle microtubules to kinetochore amigo.geneontol...
GO GO:0051313 View Gene Set 0.0001262 8 0.009266 180 attachment of spindle microtubules to chromosome amigo.geneontol...
GO GO:0045935 View Gene Set 0.0001304 680 0.009523 183 positive regulation of nucleobase nucleoside nucleotide and nucleic acid metabolic process amigo.geneontol...
GO GO:0043981 View Gene Set 0.0001327 6 0.00958 184 histone H4-K5 acetylation amigo.geneontol...
GO GO:0043982 View Gene Set 0.0001327 6 0.00958 184 histone H4-K8 acetylation amigo.geneontol...
GO GO:0003690 View Gene Set 0.0001367 99 0.009822 186 double-stranded DNA binding amigo.geneontol...
GO GO:0010628 View Gene Set 0.0001484 632 0.01036 187 positive regulation of gene expression amigo.geneontol...
GO GO:0050657 View Gene Set 0.0001491 102 0.01036 187 nucleic acid transport amigo.geneontol...
GO GO:0050658 View Gene Set 0.0001491 102 0.01036 187 RNA transport amigo.geneontol...
GO GO:0051236 View Gene Set 0.0001491 102 0.01036 187 establishment of RNA localization amigo.geneontol...
GO GO:0071564 View Gene Set 0.0001479 11 0.01036 187 npBAF complex amigo.geneontol...
GO GO:0016278 View Gene Set 0.0001519 37 0.01036 187 lysine N-methyltransferase activity amigo.geneontol...
GO GO:0016279 View Gene Set 0.0001519 37 0.01036 187 protein-lysine N-methyltransferase activity amigo.geneontol...
GO GO:0018024 View Gene Set 0.0001519 37 0.01036 187 histone-lysine N-methyltransferase activity amigo.geneontol...
GO GO:0043566 View Gene Set 0.0001517 149 0.01036 187 structure-specific DNA binding amigo.geneontol...
GO GO:0070742 View Gene Set 0.0001505 8 0.01036 187 C2H2 zinc finger domain binding amigo.geneontol...
GO GO:0010608 View Gene Set 0.0001728 247 0.01172 197 posttranscriptional regulation of gene expression amigo.geneontol...
GO GO:0030532 View Gene Set 0.0002048 32 0.0137 198 small nuclear ribonucleoprotein complex amigo.geneontol...
GO GO:0034708 View Gene Set 0.0002051 56 0.0137 198 methyltransferase complex amigo.geneontol...
GO GO:0035097 View Gene Set 0.0002051 56 0.0137 198 histone methyltransferase complex amigo.geneontol...

Gene Set Collection: Broad.c1.CYTOBAND

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad chr20q13 View Gene Set 2.826e-05 183 0.009212 1 Genes in cytogenetic band chr20q13 www.broad.mit.e...

Gene Set Collection: Broad.c2.CGP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad PUJANA_BRCA1_PCC_NETWORK View Gene Set 2.418e-33 1582 5.783e-30 1 Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of BRCA1 [Gene ID=672] across a compendium of normal tissues. www.broad.mit.e...
Broad DODD_NASOPHARYNGEAL_CARCINOMA_DN View Gene Set 6.869e-31 1253 8.216e-28 2 Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. www.broad.mit.e...
Broad PUJANA_CHEK2_PCC_NETWORK View Gene Set 4.17e-28 744 3.325e-25 3 Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient PCC >= 0.4) with that of CHEK2 [Gene ID=11200]. www.broad.mit.e...
Broad PUJANA_BRCA2_PCC_NETWORK View Gene Set 3.26e-21 410 1.95e-18 4 Genes constituting the BRCA2-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of BRCA2 [Gene ID=675] across a compendium of normal tissues. www.broad.mit.e...
Broad TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C View Gene Set 4.868e-19 436 1.941e-16 5 Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [Gene ID=407041 407042] microRNAs. www.broad.mit.e...
Broad CAIRO_HEPATOBLASTOMA_CLASSES_UP View Gene Set 4.076e-19 577 1.941e-16 5 Genes up-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). www.broad.mit.e...
Broad ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER View Gene Set 1.243e-16 138 3.749e-14 7 The 'Cervical Cancer Proliferation Cluster' (CCPC): genes whose expression in cervical carcinoma positively correlates with that of the HPV E6 and E7 oncogenes; they are also differentially expressed according to disease outcome. www.broad.mit.e...
Broad PUJANA_XPRSS_INT_NETWORK View Gene Set 1.254e-16 164 3.749e-14 7 Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1 BRCA2 ATM and CHEK2 [Gene ID=672 675 472 11200] in a compendium of normal tissues. www.broad.mit.e...
Broad KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP View Gene Set 2.891e-16 1180 7.685e-14 9 Genes up-regulated in TC71 and EWS502 cells (Ewing's sarcoma) upon knockdown of the EWSR1-FLII fusion [Gene ID=2130 2314]. www.broad.mit.e...
Broad PUJANA_ATM_PCC_NETWORK View Gene Set 6.308e-16 1375 1.395e-13 10 Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of ATM [Gene ID=472] across a compendium of normal tissues. www.broad.mit.e...
Broad WONG_EMBRYONIC_STEM_CELL_CORE View Gene Set 6.415e-16 331 1.395e-13 10 The 'core ESC-like gene module': genes coordinately up-regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module. www.broad.mit.e...
Broad MANALO_HYPOXIA_DN View Gene Set 1.011e-14 276 2.015e-12 12 Genes down-regulated in response to both hypoxia and overexpression of an active form of HIF1A [Gene ID=3091]. www.broad.mit.e...
Broad SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP View Gene Set 1.424e-14 143 2.59e-12 13 Up-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. www.broad.mit.e...
Broad KOBAYASHI_EGFR_SIGNALING_24HR_DN View Gene Set 1.516e-14 243 2.59e-12 13 Genes down-regulated in H1975 cells (non-small cell lung cancer NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. www.broad.mit.e...
Broad MITSIADES_RESPONSE_TO_APLIDIN_DN View Gene Set 2.451e-13 241 3.909e-11 15 Genes down-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164] a marine-derived compound with potential anti-cancer properties. www.broad.mit.e...
Broad CROONQUIST_NRAS_SIGNALING_DN View Gene Set 2.48e-12 62 3.49e-10 16 Genes down-regulated in ANBL-6 cell line (multiple myeloma MM) expressing a constantly active form of NRAS [Gene ID=4893] off a plasmid vector compared to those grown in the presence of IL6 [Gene ID=3569]. www.broad.mit.e...
Broad FOURNIER_ACINAR_DEVELOPMENT_LATE_2 View Gene Set 2.463e-12 265 3.49e-10 16 Genes identified by method 2 as coordinately down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. www.broad.mit.e...
Broad MARKEY_RB1_ACUTE_LOF_DN View Gene Set 3.554e-12 201 4.722e-10 18 Genes down-regulated in adult fibroblasts with inactivated RB1 [Gene ID=5925] by Cre-lox: acute loss of function (LOF) of RB1. www.broad.mit.e...
Broad BIDUS_METASTASIS_UP View Gene Set 5.452e-12 203 6.863e-10 19 Genes up-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. www.broad.mit.e...
Broad CROONQUIST_IL6_DEPRIVATION_DN View Gene Set 1.829e-11 80 2.188e-09 20 Genes down-regulated in the ANBL-6 cell line (multiple myeloma MM) after withdrawal of IL6 [Gene ID=3569]. www.broad.mit.e...
Broad MISSIAGLIA_REGULATED_BY_METHYLATION_DN View Gene Set 2.881e-11 96 3.282e-09 21 Genes down-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668] a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. www.broad.mit.e...
Broad BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP View Gene Set 3.088e-11 184 3.358e-09 22 Up-regulated genes in hepatocellular carcinoma (HCC) subclass G3 defined by unsupervised clustering. www.broad.mit.e...
Broad GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN View Gene Set 5.42e-11 51 5.637e-09 23 Genes from the turquoise module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). www.broad.mit.e...
Broad PUJANA_BRCA_CENTERED_NETWORK View Gene Set 7.647e-11 92 7.621e-09 24 Genes constituting the BRCA-centered network (BCN). www.broad.mit.e...
Broad GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN View Gene Set 2.825e-10 308 2.703e-08 25 Genes down-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [Gene ID=7764] locus only. www.broad.mit.e...
Broad LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN View Gene Set 1.248e-09 158 1.148e-07 26 Genes down-regulated in Wilm's tumor samples compared to fetal kidney. www.broad.mit.e...
Broad BERENJENO_TRANSFORMED_BY_RHOA_UP View Gene Set 3.656e-09 485 3.124e-07 27 Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [Gene ID=387] off plasmid vector. www.broad.mit.e...
Broad PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP View Gene Set 3.564e-09 53 3.124e-07 27 The XPRSS-Int network genes up-regulated in breast tumors from patients with germline mutations in BRCA1 [Gene ID=672] compared to those with the wild type allele. www.broad.mit.e...
Broad ODONNELL_TFRC_TARGETS_DN View Gene Set 6.634e-09 131 5.289e-07 29 Genes dpwn-regulated in P493-6 cells (B lymphocyte) upon knockdown of TFRC [Gene ID=7037] by RNAi. www.broad.mit.e...
Broad NUYTTEN_EZH2_TARGETS_DN View Gene Set 6.497e-09 859 5.289e-07 29 Genes down-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [Gene ID=2146] by RNAi. www.broad.mit.e...
Broad BENPORATH_CYCLING_GENES View Gene Set 1.401e-08 630 1.047e-06 31 Genes showing cell-cycle stage-specific expression [PMID=12058064]. www.broad.mit.e...
Broad MUELLER_PLURINET View Gene Set 1.384e-08 294 1.047e-06 31 Genes constituting the PluriNet protein-protein network shared by the pluripotent cells (embryonic stem cells embryonical carcinomas and induced pluripotent cells). www.broad.mit.e...
Broad ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN View Gene Set 2.032e-08 61 1.473e-06 33 Genes down-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. www.broad.mit.e...
Broad MORI_LARGE_PRE_BII_LYMPHOCYTE_UP View Gene Set 2.691e-08 52 1.893e-06 34 Up-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. www.broad.mit.e...
Broad SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 View Gene Set 3.26e-08 435 2.228e-06 35 Cluster 6 of method A: up-regulation of these genes in patients with non???small cell lung cancer (NSCLC) predicts poor survival outcome. www.broad.mit.e...
Broad FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP View Gene Set 3.465e-08 144 2.24e-06 36 Genes up-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. www.broad.mit.e...
Broad KANG_DOXORUBICIN_RESISTANCE_UP View Gene Set 3.384e-08 53 2.24e-06 36 Genes differentialy expressed in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. www.broad.mit.e...
Broad HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP View Gene Set 4.081e-08 93 2.569e-06 38 Genes up-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. www.broad.mit.e...
Broad ZHAN_MULTIPLE_MYELOMA_PR_UP View Gene Set 5.512e-08 43 3.381e-06 39 Top 50 up-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. www.broad.mit.e...
Broad GARY_CD5_TARGETS_DN View Gene Set 7.604e-08 415 4.547e-06 40 Genes down-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [Gene ID=921] off a plasmid vector. www.broad.mit.e...
Broad WHITEFORD_PEDIATRIC_CANCER_MARKERS View Gene Set 7.967e-08 92 4.648e-06 41 Differentially expressed genes in a panel of xenografts representing 8 common pediatric tumors compared to the normal tissues. www.broad.mit.e...
Broad AMUNDSON_GAMMA_RADIATION_RESPONSE View Gene Set 1.698e-07 36 9.669e-06 42 Genes down-regulated across the entire panel of NCI-60 cell lines in response to gamma radiation. www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN View Gene Set 2.318e-07 241 1.289e-05 43 Genes down-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. www.broad.mit.e...
Broad LY_AGING_OLD_DN View Gene Set 3.187e-07 47 1.732e-05 44 Genes up-regulated in fibroblasts from old individuals compared to those from young donors. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN View Gene Set 3.527e-07 920 1.875e-05 45 Genes down-regulated in HL-60 cells (acute promyelocytic leukemia APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. www.broad.mit.e...
Broad PAL_PRMT5_TARGETS_UP View Gene Set 4.462e-07 178 2.32e-05 46 Genes up-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [Gene ID=10419] by RNAi. www.broad.mit.e...
Broad MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN View Gene Set 1.225e-06 121 6.232e-05 47 Genes distinguishing in multiple myeloma (MM) samples with lower expression of TACI [Gene ID=23495]. www.broad.mit.e...
Broad ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN View Gene Set 2.84e-06 42 0.0001386 48 Genes down-regulated in P493-6 cells (B lymphocyte) by MYC [Gene ID=4609] and up-regulated by RNAi knockdown of TFRC [Gene ID=7037]. www.broad.mit.e...
Broad LY_AGING_MIDDLE_DN View Gene Set 2.813e-06 15 0.0001386 48 Genes down-regulated in fibroblasts from middle-age individuals compared to those from the young donors. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN View Gene Set 3.104e-06 832 0.0001456 50 Genes down-regulated in HL-60 cells (acute promyelocytic leukemia APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. www.broad.mit.e...
Broad WINNEPENNINCKX_MELANOMA_METASTASIS_UP View Gene Set 3.048e-06 152 0.0001456 50 Genes from the 254-gene classifier which were up-regulated in melanoma patients with a reported distant metastasis within 4 years. www.broad.mit.e...
Broad REN_BOUND_BY_E2F View Gene Set 3.405e-06 47 0.0001566 52 Genes whose promoters were bound by E2F1 [Gene ID=1869] and E2F4 [Gene ID=1874] in the primary fibroblasts WI-38 by ChIP on chip assay. www.broad.mit.e...
Broad RIZ_ERYTHROID_DIFFERENTIATION View Gene Set 3.521e-06 71 0.0001589 53 Selected gradually up-regulated genes in the TLX1 [Gene ID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP View Gene Set 4.151e-06 135 0.0001839 54 Top 200 marker genes up-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation high levels of serum AFP [Gene ID=174] and chromosomal instability. www.broad.mit.e...
Broad DAZARD_RESPONSE_TO_UV_NHEK_DN View Gene Set 4.999e-06 256 0.0002174 55 Genes down-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. www.broad.mit.e...
Broad BLUM_RESPONSE_TO_SALIRASIB_DN View Gene Set 5.276e-06 332 0.0002254 56 Selected genes down-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [Gene ID=3265]. www.broad.mit.e...
Broad EGUCHI_CELL_CYCLE_RB1_TARGETS View Gene Set 8.241e-06 19 0.0003458 57 RB1 [Gene ID=5925] target genes involved in cell cycle regulation: genes down-regulated by doxorubicin [PubChem=31703] only in cells expressing RB1. www.broad.mit.e...
Broad GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN View Gene Set 8.803e-06 160 0.0003631 58 Genes down-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2 STK6 and ZNF217 [Gene ID=4605 6790 7764] www.broad.mit.e...
Broad RUIZ_TNC_TARGETS_DN View Gene Set 1.032e-05 138 0.0004185 59 Genes down-regulated in T98G cells (glioblastoma) by TNC [Gene ID=3371]. www.broad.mit.e...
Broad MORI_IMMATURE_B_LYMPHOCYTE_DN View Gene Set 1.54e-05 52 0.0006141 60 Down-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. www.broad.mit.e...
Broad VECCHI_GASTRIC_CANCER_EARLY_UP View Gene Set 1.604e-05 408 0.0006289 61 Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. www.broad.mit.e...
Broad LEE_EARLY_T_LYMPHOCYTE_UP View Gene Set 1.778e-05 80 0.000686 62 Genes up-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. www.broad.mit.e...
Broad MATTIOLI_MGUS_VS_PCL View Gene Set 1.885e-05 109 0.0007156 63 Genes changed in MGUS (monoclonal gammopathy of undetermined significance) compared to PCL (plasma cell leukemia) samples. www.broad.mit.e...
Broad RIZ_ERYTHROID_DIFFERENTIATION_CCNE1 View Gene Set 2.107e-05 38 0.0007876 64 Selected gradually up-regulated genes whose expression profile follows that of CCNE1 [Gene ID=898] in the TLX1 [Gene ID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). www.broad.mit.e...
Broad LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER View Gene Set 2.249e-05 167 0.0008277 65 Overexpressed genes with amplified copy number across 27 non-small cell lung cancer (NSCLC) cell lines. www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP View Gene Set 2.551e-05 220 0.0009247 66 Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. www.broad.mit.e...
Broad MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP View Gene Set 3.766e-05 92 0.001345 67 Genes correlated with the early tumor onset in the Emu-myc transgenic mouse lymphoma model. www.broad.mit.e...
Broad GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP View Gene Set 4.84e-05 180 0.001678 68 Genes up-regulated in quiescent CD34+ [Gene ID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. www.broad.mit.e...
Broad SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC View Gene Set 4.825e-05 101 0.001678 68 Cluster 2: genes up-regulated in B493-6 cells (B lymphocytes) by serum alone or in combination with MYC [Gene ID=4609] but not by MYC alone. www.broad.mit.e...
Broad HORIUCHI_WTAP_TARGETS_DN View Gene Set 5.628e-05 289 0.001919 70 Genes down-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [Gene ID=9589] by RNAi. www.broad.mit.e...
Broad MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN View Gene Set 5.697e-05 18 0.001919 70 Genes down-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). www.broad.mit.e...
Broad ZHANG_BREAST_CANCER_PROGENITORS_UP View Gene Set 5.863e-05 370 0.001948 72 Genes changed in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. www.broad.mit.e...
Broad FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN View Gene Set 6.305e-05 43 0.002066 73 Genes down-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen raloxifene or ICI 182780 but not by estradiol [PubChem=44959 5035 3478439 5757]. www.broad.mit.e...
Broad BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP View Gene Set 7.129e-05 44 0.002304 74 Up-regulated genes in hepatocellular carcinoma (HCC) subclass G123 defined by unsupervised clustering. www.broad.mit.e...
Broad HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2 View Gene Set 8.483e-05 10 0.002705 75 Genes distinguishing between breast cancer tumors bearing mutations in BRCA1 [Gene ID=672] and those with mutated BRCA2 [Gene ID=675]. www.broad.mit.e...
Broad SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP View Gene Set 8.71e-05 269 0.002714 76 Genes up-regulated in nsopharyngeal carcinoma relative to the normal tissue. www.broad.mit.e...
Broad SMID_BREAST_CANCER_LUMINAL_A_DN View Gene Set 8.738e-05 17 0.002714 76 Genes down-regulated in the luminal A subtype of breast cancer. www.broad.mit.e...
Broad KALMA_E2F1_TARGETS View Gene Set 9.652e-05 11 0.00296 78 DNA replication genes up-regulated in a Rat-1a cell line (fibroblast) by expression of E2F1 [Gene ID=1869]. www.broad.mit.e...
Broad COLDREN_GEFITINIB_RESISTANCE_UP View Gene Set 0.0001268 74 0.003804 79 Genes up-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. www.broad.mit.e...
Broad SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP View Gene Set 0.0001272 16 0.003804 79 Genes up-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial basal-like phenotype) confluency. www.broad.mit.e...
Broad SHEPARD_CRUSH_AND_BURN_MUTANT_DN View Gene Set 0.0001403 147 0.004143 81 Human orthologs of genes down-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [Gene ID=4605]. www.broad.mit.e...
Broad TIEN_INTESTINE_PROBIOTICS_24HR_UP View Gene Set 0.0001895 537 0.005435 82 Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. www.broad.mit.e...
Broad FARMER_BREAST_CANCER_CLUSTER_2 View Gene Set 0.0001863 33 0.005435 82 Cluster 2: selected proliferation and 8q amplicon genes clustered together across breast cancer samples. www.broad.mit.e...
Broad PUJANA_BREAST_CANCER_LIT_INT_NETWORK View Gene Set 0.0001913 100 0.005435 82 Genes constituting the LIT-Int network of proteins interacting with breast cancer reference proteins BRCA1 BRCA2 ATM and CHEK2 [Gene ID=672 675 472 11200]; the interactions were manually curated from the literature. www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_DN View Gene Set 0.0001931 250 0.005435 82 Genes down-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. www.broad.mit.e...
Broad SEMBA_FHIT_TARGETS_DN View Gene Set 0.0002386 10 0.006636 86 Genes down-regulated in H1299 cells (non-small cell lung cancer NSCLC) expressing the Y144F mutant form of FHIT [Gene ID=2272]. www.broad.mit.e...
Broad DANG_MYC_TARGETS_UP View Gene Set 0.0002758 127 0.007584 87 Genes up-regulated by MYC [Gene ID=4609] and whose promoters are bound by MYC according to MYC Target Gene Database. www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN View Gene Set 0.0002817 46 0.007657 88 Cluster 6: genes down-regulated in B493-6 cells (B lymphocytes) by MYC [Gene ID=4609] in combination with serum but not affected by serum alone; they are also up-regulated by MYC alone. www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP View Gene Set 0.0003114 36 0.008275 89 Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN View Gene Set 0.0003114 36 0.008275 89 Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. www.broad.mit.e...
Broad DAZARD_UV_RESPONSE_CLUSTER_G6 View Gene Set 0.0003351 122 0.008807 91 Cluster G6: genes increasingly down-regulated in NHEK cells (normal keratinocyte) after UV-B irradiation. www.broad.mit.e...
Broad GEORGES_CELL_CYCLE_MIR192_TARGETS View Gene Set 0.0003409 59 0.008862 92 Experimentally validated direct targets of MIR192 [Gene ID=406967] microRNA; MIR192 caused cell cycle arrest in HCT116 cells (colon cancer). www.broad.mit.e...
Broad CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP View Gene Set 0.000361 135 0.009187 93 Genes up-regulated in CD4+ [Gene ID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. www.broad.mit.e...
Broad SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP View Gene Set 0.0003574 469 0.009187 93 Genes up-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. www.broad.mit.e...
Broad MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN View Gene Set 0.0003796 212 0.009558 95 Genes down-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. www.broad.mit.e...
Broad MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN View Gene Set 0.0003865 42 0.009631 96 Genes down-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI [Gene ID=23495]. www.broad.mit.e...
Broad WEI_MYCN_TARGETS_WITH_E_BOX View Gene Set 0.0004034 757 0.009902 97 Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [Gene ID=4613]. www.broad.mit.e...
Broad TARTE_PLASMA_CELL_VS_PLASMABLAST_DN View Gene Set 0.0004057 303 0.009902 97 Genes down-regulated in mature plasma cells compared with plasmablastic B lymphocytes. www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON View Gene Set 0.0004245 134 0.01026 99 Genes within amplicon 20q12-q13 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad FINETTI_BREAST_CANCER_KINOME_RED View Gene Set 0.0004507 15 0.01067 100 Genes in the red cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. www.broad.mit.e...
Broad FINETTI_BREAST_CANCER_BASAL_VS_LUMINAL View Gene Set 0.0004507 15 0.01067 100 Protein kinases distinguishing between basal and luminal A subtypes of breast cancer. www.broad.mit.e...
Broad BASAKI_YBX1_TARGETS_UP View Gene Set 0.0004967 279 0.01165 102 Genes up-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [Gene ID=4904] knockdown by RNAi. www.broad.mit.e...
Broad PENG_GLUTAMINE_DEPRIVATION_DN View Gene Set 0.0005091 84 0.01182 103 Genes down-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. www.broad.mit.e...
Broad GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN View Gene Set 0.0005532 86 0.01272 104 Genes down-regulated in quiescent vs dividing CD34+ [Gene ID=8842] cells isolated from peripheral blood of normal donors. www.broad.mit.e...
Broad BENPORATH_ES_CORE_NINE_CORRELATED View Gene Set 0.0006937 100 0.0158 105 Breast cancer compendium: 100 transcription regulators showing most correlated expression with the 9 'embryonic stem cell' transcription factors that are preferentially and coordinately overexpressed in the high-grade ER-negative breast cancer tumors. www.broad.mit.e...
Broad SHEN_SMARCA2_TARGETS_UP View Gene Set 0.000713 406 0.01609 106 Genes whose expression positively correlated with that of SMARCA2 [Gene ID=6595] in prostate cancer samples. www.broad.mit.e...
Broad SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN View Gene Set 0.0007274 22 0.01626 107 Cell cycle genes changed in H1299 cells (lung cancer) after overexpression of either P53 [Gene ID=7157] or P73 [Gene ID=7161]. www.broad.mit.e...
Broad YU_MYC_TARGETS_UP View Gene Set 0.0007706 37 0.01707 108 Genes up-regulated in B cell lymphoma tumors expressing an activated form of MYC [Gene ID=4609]. www.broad.mit.e...
Broad GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN View Gene Set 0.0008883 148 0.01949 109 Genes down-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [Gene ID=2313 190] by RNAi. www.broad.mit.e...
Broad KAUFFMANN_DNA_REPAIR_GENES View Gene Set 0.0009753 205 0.02121 110 Genes involved in DNA repair compiled manually by the authors. www.broad.mit.e...
Broad BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN View Gene Set 0.001006 7 0.02168 111 Genes down-regulated in A172 cells (glioma does not express MGMT [Gene ID=4255]) by carmustine [PubChem=2578] at 24 h. www.broad.mit.e...
Broad LY_AGING_PREMATURE_DN View Gene Set 0.001034 24 0.02207 112 Genes down-regulated in fibroblasts from patients with Hutchinson-Gilford progeria (premature aging) compared to those from normal young individuals. www.broad.mit.e...
Broad CHANG_CYCLING_GENES View Gene Set 0.001068 49 0.02261 113 Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. www.broad.mit.e...
Broad MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP View Gene Set 0.001156 10 0.02425 114 Up-regulated genes predicting poor survival of patients with thyroid carcinoma. www.broad.mit.e...
Broad LE_EGR2_TARGETS_UP View Gene Set 0.001346 100 0.028 115 Genes up-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [Gene ID=1959]. www.broad.mit.e...
Broad GRADE_COLON_CANCER_UP View Gene Set 0.001429 711 0.02948 116 Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. www.broad.mit.e...
Broad GENTILE_UV_RESPONSE_CLUSTER_D4 View Gene Set 0.001451 49 0.02967 117 Cluster d4: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h after irradiation with high dose UV-C. www.broad.mit.e...
Broad XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN View Gene Set 0.001465 17 0.02969 118 Genes down-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [Gene ID=207] upon exposure to HGF [Gene ID=3082] for 48 hr. www.broad.mit.e...
Broad WELCSH_BRCA1_TARGETS_1_DN View Gene Set 0.001536 124 0.03087 119 Upregulated by induction of exogenous BRCA1 in EcR-293 cells www.broad.mit.e...
Broad RHODES_UNDIFFERENTIATED_CANCER View Gene Set 0.001582 60 0.03154 120 Genes commonly up-regulated in undifferentiated cancer relative to well-differentiated cancer based on the meta-analysis of the OncoMine gene expression database. www.broad.mit.e...
Broad FURUKAWA_DUSP6_TARGETS_PCI35_DN View Gene Set 0.001637 66 0.03237 121 Genes down-regulated in PCI-35 cells (pancreatic cancer lack endogenous DUSP6 [Gene ID=1848]) upon expression of DUSP6 off an adenoviral vector. www.broad.mit.e...
Broad RAMALHO_STEMNESS_UP View Gene Set 0.001842 192 0.03612 122 Genes enriched in embryonic neural and hematopoietic stem cells. www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM View Gene Set 0.002117 154 0.04117 123 Cluster 7: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [Gene ID=4609] and down-regulated by the combination of MYC and serum. www.broad.mit.e...
Broad AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP View Gene Set 0.002385 288 0.046 124 Up-regulated genes whose expression correlates with copy number gains in pancreatic adenocarcinoma cell lines and primary tumor specimens. www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.BIOCARTA

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad BIOCARTA_CARM_ER_PATHWAY View Gene Set 8.049e-05 35 0.01747 1 CARM1 and Regulation of the Estrogen Receptor www.broad.mit.e...
Broad BIOCARTA_RANMS_PATHWAY View Gene Set 0.0002789 10 0.03026 2 Role of Ran in mitotic spindle regulation www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.KEGG

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad KEGG_SPLICEOSOME View Gene Set 2.326e-08 118 4.326e-06 1 Spliceosome www.broad.mit.e...
Broad KEGG_RNA_DEGRADATION View Gene Set 7.784e-06 59 0.0007239 2 RNA degradation www.broad.mit.e...
Broad KEGG_CELL_CYCLE View Gene Set 2.745e-05 128 0.001702 3 Cell cycle www.broad.mit.e...
Broad KEGG_BASE_EXCISION_REPAIR View Gene Set 0.0001001 35 0.004652 4 Base excision repair www.broad.mit.e...
Broad KEGG_DNA_REPLICATION View Gene Set 0.001159 36 0.04313 5 DNA replication www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.REACTOME

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA View Gene Set 6.464e-10 128 2.78e-07 1 Genes involved in Processing of Capped Intron-Containing Pre-mRNA www.broad.mit.e...
Broad REACTOME_MRNA_SPLICING View Gene Set 4.305e-09 97 9.257e-07 2 Genes involved in mRNA Splicing www.broad.mit.e...
Broad REACTOME_MITOTIC_M_M_G1_PHASES View Gene Set 8.423e-09 157 1.207e-06 3 Genes involved in Mitotic M-M/G1 phases www.broad.mit.e...
Broad REACTOME_ELONGATION_AND_PROCESSING_OF_CAPPED_TRANSCRIPTS View Gene Set 1.839e-08 124 1.977e-06 4 Genes involved in Elongation and Processing of Capped Transcripts www.broad.mit.e...
Broad REACTOME_GENE_EXPRESSION View Gene Set 3.244e-08 415 2.79e-06 5 Genes involved in Gene Expression www.broad.mit.e...
Broad REACTOME_METABOLISM_OF_RNA View Gene Set 7.186e-08 95 5.15e-06 6 Genes involved in Metabolism of RNA www.broad.mit.e...
Broad REACTOME_FORMATION_AND_MATURATION_OF_MRNA_TRANSCRIPT View Gene Set 1.028e-07 142 6.314e-06 7 Genes involved in Formation and Maturation of mRNA Transcript www.broad.mit.e...
Broad REACTOME_MITOTIC_PROMETAPHASE View Gene Set 2.446e-07 92 1.315e-05 8 Genes involved in Mitotic Prometaphase www.broad.mit.e...
Broad REACTOME_CELL_CYCLE_MITOTIC View Gene Set 6.363e-07 306 3.04e-05 9 Genes involved in Cell Cycle Mitotic www.broad.mit.e...
Broad REACTOME_DEADENYLATION_OF_MRNA View Gene Set 4.108e-06 21 0.0001767 10 Genes involved in Deadenylation of mRNA www.broad.mit.e...
Broad REACTOME_METABOLISM_OF_MRNA View Gene Set 1.272e-05 45 0.0004971 11 Genes involved in Metabolism of mRNA www.broad.mit.e...
Broad REACTOME_SNRNP_ASSEMBLY View Gene Set 0.0005486 50 0.01966 12 Genes involved in snRNP Assembly www.broad.mit.e...
Broad REACTOME_INACTIVATION_OF_APC_VIA_DIRECT_INHIBITION_OF_THE_APCOMPLEX View Gene Set 0.001055 18 0.0324 13 Genes involved in Inactivation of APC/C via direct inhibition of the APC/C complex www.broad.mit.e...
Broad REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRON_CONTAINING_TRANSCRIPT View Gene Set 0.001021 42 0.0324 13 Genes involved in Transport of Mature mRNA derived from an Intron-Containing Transcript www.broad.mit.e...
Broad REACTOME_CELL_CYCLE_CHECKPOINTS View Gene Set 0.001403 110 0.04021 15 Genes involved in Cell Cycle Checkpoints www.broad.mit.e...
Broad REACTOME_REV_MEDIATED_NUCLEAR_EXPORT_OF_HIV1_RNA View Gene Set 0.001555 31 0.04052 16 Genes involved in Rev-mediated nuclear export of HIV-1 RNA www.broad.mit.e...
Broad REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS View Gene Set 0.001602 29 0.04052 16 Genes involved in Transport of Ribonucleoproteins into the Host Nucleus www.broad.mit.e...
Broad REACTOME_NUCLEAR_IMPORT_OF_REV_PROTEIN View Gene Set 0.001754 30 0.0419 18 Genes involved in Nuclear import of Rev protein www.broad.mit.e...
Broad REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY View Gene Set 0.002192 29 0.04961 19 Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery www.broad.mit.e...

Gene Set Collection: Broad.c3.TFT

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad GCCATNTTG_V$YY1_Q6 View Gene Set 2.084e-13 289 1.282e-10 1 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif GCCATNTTG which matches annotation for YY1: YY1 transcription factor www.broad.mit.e...
Broad V$NFMUE1_Q6 View Gene Set 1.591e-11 175 4.893e-09 2 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif CGGCCATCT. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F_Q6 View Gene Set 4.641e-08 165 9.514e-06 3 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGS. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F1_Q6 View Gene Set 6.576e-08 167 1.011e-05 4 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGS which matches annotation for E2F1: E2F transcription factor 1 www.broad.mit.e...
Broad V$E2F_Q4 View Gene Set 1.969e-07 166 2.422e-05 5 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGS. Motif does not match any known transcription factor www.broad.mit.e...
Broad TAANNYSGCG_UNKNOWN View Gene Set 5.75e-07 60 5.894e-05 6 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TAANNYSGCG. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F1_Q4_01 View Gene Set 1.054e-06 167 9.259e-05 7 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGSG which matches annotation for E2F<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad V$YY1_02 View Gene Set 1.951e-06 168 0.0001333 8 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNNCGGCCATCTTGNCTSNW which matches annotation for YY1: YY1 transcription factor www.broad.mit.e...
Broad V$E2F1_Q6_01 View Gene Set 1.795e-06 177 0.0001333 8 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NTTTCGCGCS which matches annotation for E2F1: E2F transcription factor 1 www.broad.mit.e...
Broad RCGCANGCGY_V$NRF1_Q6 View Gene Set 3.284e-06 580 0.0002019 10 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif RCGCANGCGY which matches annotation for NRF1: nuclear respiratory factor 1 www.broad.mit.e...
Broad V$E2F_02 View Gene Set 4.257e-06 169 0.0002312 11 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGC. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F_Q3_01 View Gene Set 4.512e-06 171 0.0002312 11 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGSG which matches annotation for E2F<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad V$E2F1DP1_01 View Gene Set 7.776e-06 169 0.0003188 13 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTCSCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad V$E2F1DP2_01 View Gene Set 7.776e-06 169 0.0003188 13 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSSCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP2: transcription factor Dp-2 (E2F dimerization partner 2) www.broad.mit.e...
Broad V$E2F4DP2_01 View Gene Set 7.776e-06 169 0.0003188 13 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTCSCGC which matches annotation for E2F4: E2F transcription factor 4 p107/p130-binding<br> TFDP2: transcription factor Dp-2 (E2F dimerization partner 2) www.broad.mit.e...
Broad V$YY1_Q6 View Gene Set 8.43e-06 166 0.000324 16 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif GCCATNTTN which matches annotation for YY1: YY1 transcription factor www.broad.mit.e...
Broad TCCCRNNRTGC_UNKNOWN View Gene Set 1.532e-05 130 0.0005541 17 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TCCCRNNRTGC. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F1_Q4 View Gene Set 1.735e-05 178 0.0005673 18 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NTTSGCGG which matches annotation for E2F1: E2F transcription factor 1 www.broad.mit.e...
Broad V$E2F_Q4_01 View Gene Set 1.753e-05 171 0.0005673 18 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NCSCGCSAAAN which matches annotation for E2F<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad KCCGNSWTTT_UNKNOWN View Gene Set 2.144e-05 76 0.0006591 20 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif KCCGNSWTTT. Motif does not match any known transcription factor www.broad.mit.e...
Broad SGCGSSAAA_V$E2F1DP2_01 View Gene Set 2.339e-05 122 0.0006849 21 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif SGCGSSAAA which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1<br> RB1: retinoblastoma 1 (including osteosarcoma) www.broad.mit.e...
Broad GGCNKCCATNK_UNKNOWN View Gene Set 2.834e-05 84 0.0007923 22 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif GGCNKCCATNK. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$NRF1_Q6 View Gene Set 7.771e-05 151 0.002078 23 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif CGCATGCGCR which matches annotation for NRF1: nuclear respiratory factor 1 www.broad.mit.e...
Broad AAGWWRNYGGC_UNKNOWN View Gene Set 0.0001239 85 0.00293 24 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif AAGWWRNYGGC. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F4DP1_01 View Gene Set 0.0001149 174 0.00293 24 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGC which matches annotation for E2F4: E2F transcription factor 4 p107/p130-binding<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad V$E2F_Q6_01 View Gene Set 0.0001226 167 0.00293 24 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NKCGCGCSAAAN which matches annotation for E2F<br> TFDP1: transcription factor Dp-1 www.broad.mit.e...
Broad ACAWNRNSRCGG_UNKNOWN View Gene Set 0.0001337 50 0.003046 27 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif ACAWNRNSRCGG. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F_Q3 View Gene Set 0.0001456 162 0.003089 28 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTCGCGC. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F1_Q3 View Gene Set 0.0001454 176 0.003089 28 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NKTSSCGC which matches annotation for E2F1: E2F transcription factor 1 www.broad.mit.e...
Broad V$GABP_B View Gene Set 0.0001866 162 0.003826 30 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif VCCGGAAGNGCR which matches annotation for GABPA: GA binding protein transcription factor alpha subunit 60kDa<br> GABPB2: GA binding protein transcription factor beta subunit 2 www.broad.mit.e...
Broad V$E2F1DP1RB_01 View Gene Set 0.00025 168 0.004959 31 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1<br> RB1: retinoblastoma 1 (including osteosarcoma) www.broad.mit.e...
Broad GGCKCATGS_UNKNOWN View Gene Set 0.0004913 43 0.009442 32 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif GGCKCATGS. Motif does not match any known transcription factor www.broad.mit.e...
Broad GATGKMRGCG_UNKNOWN View Gene Set 0.0006567 47 0.01224 33 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif GATGKMRGCG. Motif does not match any known transcription factor www.broad.mit.e...
Broad TGCGCANK_UNKNOWN View Gene Set 0.000829 361 0.015 34 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TGCGCANK. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$MYCMAX_01 View Gene Set 0.0009043 189 0.01589 35 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNACCACGTGGTNN which matches annotation for MYC: v-myc myelocytomatosis viral oncogene homolog (avian)<br> MAX: MYC associated factor X www.broad.mit.e...
Broad GCGSCMNTTT_UNKNOWN View Gene Set 0.001112 49 0.019 36 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif GCGSCMNTTT. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$E2F_03 View Gene Set 0.001329 171 0.02209 37 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGCGMNR. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$AP2_Q6 View Gene Set 0.00152 188 0.0246 38 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif MKCCCSCNGGCG which matches annotation for GTF3A: general transcription factor IIIA www.broad.mit.e...
Broad V$ZF5_B View Gene Set 0.002213 184 0.03489 39 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NRNGNGCGCGCWN which matches annotation for ZFP161: zinc finger protein 161 homolog (mouse) www.broad.mit.e...
Broad V$ELK1_02 View Gene Set 0.002339 170 0.03596 40 Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNNNCCGGAARTNN which matches annotation for ELK1: ELK1 member of ETS oncogene family www.broad.mit.e...
Broad KMCATNNWGGA_UNKNOWN View Gene Set 0.002592 60 0.03888 41 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif KMCATNNWGGA. Motif does not match any known transcription factor www.broad.mit.e...
Broad V$MZF1_02 View Gene Set 0.003057 175 0.04476 42 Genes with promoter regions [-2kb 2kb] around transcription start site containing motif KNNNKAGGGGNAA. Motif does not match any known transcription factor www.broad.mit.e...

Gene Set Collection: Broad.c4.CGN

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad GNF2_CCNA2 View Gene Set 1.607e-18 62 6.862e-16 1 Neighborhood of CCNA2 www.broad.mit.e...
Broad GNF2_CCNB2 View Gene Set 2.525e-17 53 5.392e-15 2 Neighborhood of CCNB2 www.broad.mit.e...
Broad GNF2_PCNA View Gene Set 9.5e-17 62 1.352e-14 3 Neighborhood of PCNA www.broad.mit.e...
Broad GNF2_CDC20 View Gene Set 1.687e-16 52 1.8e-14 4 Neighborhood of CDC20 www.broad.mit.e...
Broad GNF2_CDC2 View Gene Set 3.012e-16 56 2.572e-14 5 Neighborhood of CDC2 www.broad.mit.e...
Broad GNF2_CENPF View Gene Set 4.761e-15 56 2.904e-13 6 Neighborhood of CENPF www.broad.mit.e...
Broad GNF2_SMC4L1 View Gene Set 4.258e-15 75 2.904e-13 6 Neighborhood of SMC4L1 www.broad.mit.e...
Broad GNF2_RRM1 View Gene Set 8.683e-15 82 4.635e-13 8 Neighborhood of RRM1 www.broad.mit.e...
Broad MORF_BUB3 View Gene Set 1.136e-14 256 5.392e-13 9 Neighborhood of BUB3 www.broad.mit.e...
Broad GNF2_HMMR View Gene Set 4.461e-14 43 1.905e-12 10 Neighborhood of HMMR www.broad.mit.e...
Broad MORF_HDAC2 View Gene Set 6.069e-14 256 2.356e-12 11 Neighborhood of HDAC2 www.broad.mit.e...
Broad GNF2_BUB1B View Gene Set 6.972e-14 46 2.481e-12 12 Neighborhood of BUB1B www.broad.mit.e...
Broad GNF2_RRM2 View Gene Set 1.345e-13 36 4.416e-12 13 Neighborhood of RRM2 www.broad.mit.e...
Broad MORF_PRKDC View Gene Set 4.201e-13 173 1.196e-11 14 Neighborhood of PRKDC www.broad.mit.e...
Broad MORF_RAD23A View Gene Set 4.036e-13 316 1.196e-11 14 Neighborhood of RAD23A www.broad.mit.e...
Broad GNF2_ESPL1 View Gene Set 7.39e-13 35 1.971e-11 16 Neighborhood of ESPL1 www.broad.mit.e...
Broad GNF2_DEK View Gene Set 7.845e-13 45 1.971e-11 16 Neighborhood of DEK www.broad.mit.e...
Broad MORF_ACP1 View Gene Set 1.294e-12 178 3.01e-11 18 Neighborhood of ACP1 www.broad.mit.e...
Broad GNF2_MCM5 View Gene Set 1.339e-12 51 3.01e-11 18 Neighborhood of MCM5 www.broad.mit.e...
Broad GNF2_PA2G4 View Gene Set 1.948e-12 73 4.158e-11 20 Neighborhood of PA2G4 www.broad.mit.e...
Broad MORF_AATF View Gene Set 6.098e-12 179 1.24e-10 21 Neighborhood of AATF www.broad.mit.e...
Broad GNF2_TTK View Gene Set 1.292e-11 34 2.509e-10 22 Neighborhood of TTK www.broad.mit.e...
Broad GNF2_MCM4 View Gene Set 1.369e-11 50 2.541e-10 23 Neighborhood of MCM4 www.broad.mit.e...
Broad GNF2_APEX1 View Gene Set 2.594e-11 72 4.615e-10 24 Neighborhood of APEX1 www.broad.mit.e...
Broad GNF2_MKI67 View Gene Set 4.257e-11 26 7.27e-10 25 Neighborhood of MKI67 www.broad.mit.e...
Broad MORF_FBL View Gene Set 4.563e-11 121 7.494e-10 26 Neighborhood of FBL www.broad.mit.e...
Broad MORF_UBE2I View Gene Set 4.764e-11 208 7.534e-10 27 Neighborhood of UBE2I www.broad.mit.e...
Broad MORF_DDB1 View Gene Set 5.513e-11 220 8.407e-10 28 Neighborhood of DDB1 www.broad.mit.e...
Broad MORF_DNMT1 View Gene Set 6.099e-11 105 8.98e-10 29 Neighborhood of DNMT1 www.broad.mit.e...
Broad GNF2_RFC4 View Gene Set 1.502e-10 57 2.138e-09 30 Neighborhood of RFC4 www.broad.mit.e...
Broad MORF_ANP32B View Gene Set 1.82e-10 174 2.507e-09 31 Neighborhood of ANP32B www.broad.mit.e...
Broad MORF_PCNA View Gene Set 1.967e-10 71 2.625e-09 32 Neighborhood of PCNA www.broad.mit.e...
Broad MORF_GNB1 View Gene Set 2.458e-10 276 3.181e-09 33 Neighborhood of GNB1 www.broad.mit.e...
Broad GNF2_CENPE View Gene Set 2.602e-10 37 3.267e-09 34 Neighborhood of CENPE www.broad.mit.e...
Broad GNF2_H2AFX View Gene Set 4.734e-10 28 5.776e-09 35 Neighborhood of H2AFX www.broad.mit.e...
Broad MORF_EIF3S2 View Gene Set 4.964e-10 220 5.888e-09 36 Neighborhood of EIF3S2 www.broad.mit.e...
Broad MORF_BUB1B View Gene Set 6.178e-10 61 7.13e-09 37 Neighborhood of BUB1B www.broad.mit.e...
Broad GNF2_FEN1 View Gene Set 6.364e-10 49 7.152e-09 38 Neighborhood of FEN1 www.broad.mit.e...
Broad MORF_RAD54L View Gene Set 1.145e-09 94 1.253e-08 39 Neighborhood of RAD54L www.broad.mit.e...
Broad MORF_PRKAG1 View Gene Set 1.579e-09 202 1.686e-08 40 Neighborhood of PRKAG1 www.broad.mit.e...
Broad MORF_XRCC5 View Gene Set 2.169e-09 210 2.258e-08 41 Neighborhood of XRCC5 www.broad.mit.e...
Broad MORF_DEK View Gene Set 2.497e-09 229 2.539e-08 42 Neighborhood of DEK www.broad.mit.e...
Broad MORF_RPA2 View Gene Set 2.803e-09 170 2.784e-08 43 Neighborhood of RPA2 www.broad.mit.e...
Broad MORF_ESPL1 View Gene Set 3.149e-09 58 3.056e-08 44 Neighborhood of ESPL1 www.broad.mit.e...
Broad GNF2_CKS2 View Gene Set 4.12e-09 45 3.91e-08 45 Neighborhood of CKS2 www.broad.mit.e...
Broad MORF_CSNK2B View Gene Set 6.147e-09 256 5.706e-08 46 Neighborhood of CSNK2B www.broad.mit.e...
Broad MORF_G22P1 View Gene Set 7.503e-09 145 6.816e-08 47 Neighborhood of G22P1 www.broad.mit.e...
Broad MORF_RFC4 View Gene Set 8.413e-09 137 7.484e-08 48 Neighborhood of RFC4 www.broad.mit.e...
Broad GNF2_HDAC1 View Gene Set 1.381e-08 85 1.203e-07 49 Neighborhood of HDAC1 www.broad.mit.e...
Broad GNF2_RFC3 View Gene Set 1.765e-08 38 1.508e-07 50 Neighborhood of RFC3 www.broad.mit.e...
Broad MORF_BUB1 View Gene Set 1.986e-08 49 1.662e-07 51 Neighborhood of BUB1 www.broad.mit.e...
Broad GNF2_KPNB1 View Gene Set 4.812e-08 52 3.951e-07 52 Neighborhood of KPNB1 www.broad.mit.e...
Broad GNF2_SMC2L1 View Gene Set 5.474e-08 30 4.41e-07 53 Neighborhood of SMC2L1 www.broad.mit.e...
Broad GNF2_HAT1 View Gene Set 8.494e-08 45 6.716e-07 54 Neighborhood of HAT1 www.broad.mit.e...
Broad GNF2_DENR View Gene Set 9.259e-08 39 7.189e-07 55 Neighborhood of DENR www.broad.mit.e...
Broad GNF2_ANP32B View Gene Set 1.073e-07 29 8.182e-07 56 Neighborhood of ANP32B www.broad.mit.e...
Broad GNF2_TDG View Gene Set 1.147e-07 23 8.594e-07 57 Neighborhood of TDG www.broad.mit.e...
Broad MORF_SOD1 View Gene Set 1.833e-07 247 1.35e-06 58 Neighborhood of SOD1 www.broad.mit.e...
Broad GCM_DENR View Gene Set 1.952e-07 40 1.412e-06 59 Neighborhood of DENR www.broad.mit.e...
Broad MORF_PPP1CC View Gene Set 2.548e-07 150 1.813e-06 60 Neighborhood of PPP1CC www.broad.mit.e...
Broad MORF_PHB View Gene Set 2.692e-07 112 1.884e-06 61 Neighborhood of PHB www.broad.mit.e...
Broad GNF2_ELAC2 View Gene Set 2.89e-07 32 1.99e-06 62 Neighborhood of ELAC2 www.broad.mit.e...
Broad GNF2_CKS1B View Gene Set 4.905e-07 36 3.324e-06 63 Neighborhood of CKS1B www.broad.mit.e...
Broad MORF_RRM1 View Gene Set 5.349e-07 90 3.568e-06 64 Neighborhood of RRM1 www.broad.mit.e...
Broad MORF_CDC16 View Gene Set 5.69e-07 67 3.738e-06 65 Neighborhood of CDC16 www.broad.mit.e...
Broad MORF_HDAC1 View Gene Set 6.347e-07 222 4.106e-06 66 Neighborhood of HDAC1 www.broad.mit.e...
Broad GNF2_FBL View Gene Set 6.615e-07 119 4.216e-06 67 Neighborhood of FBL www.broad.mit.e...
Broad MORF_MSH2 View Gene Set 7.827e-07 52 4.915e-06 68 Neighborhood of MSH2 www.broad.mit.e...
Broad GNF2_RAN View Gene Set 1.049e-06 78 6.489e-06 69 Neighborhood of RAN www.broad.mit.e...
Broad MORF_CTBP1 View Gene Set 1.39e-06 149 8.48e-06 70 Neighborhood of CTBP1 www.broad.mit.e...
Broad MORF_HAT1 View Gene Set 1.459e-06 155 8.777e-06 71 Neighborhood of HAT1 www.broad.mit.e...
Broad GNF2_BUB1 View Gene Set 1.861e-06 25 1.104e-05 72 Neighborhood of BUB1 www.broad.mit.e...
Broad MORF_RAF1 View Gene Set 2.114e-06 94 1.237e-05 73 Neighborhood of RAF1 www.broad.mit.e...
Broad MORF_TERF1 View Gene Set 2.486e-06 57 1.435e-05 74 Neighborhood of TERF1 www.broad.mit.e...
Broad GNF2_MSH2 View Gene Set 3.553e-06 26 2.023e-05 75 Neighborhood of MSH2 www.broad.mit.e...
Broad MORF_FANCG View Gene Set 3.881e-06 148 2.18e-05 76 Neighborhood of FANCG www.broad.mit.e...
Broad MORF_SMC1L1 View Gene Set 4.443e-06 47 2.464e-05 77 Neighborhood of SMC1L1 www.broad.mit.e...
Broad MORF_SNRP70 View Gene Set 4.687e-06 50 2.563e-05 78 Neighborhood of SNRP70 www.broad.mit.e...
Broad GNF2_XRCC5 View Gene Set 4.742e-06 61 2.563e-05 78 Neighborhood of XRCC5 www.broad.mit.e...
Broad GNF2_RBBP6 View Gene Set 5.087e-06 54 2.715e-05 80 Neighborhood of RBBP6 www.broad.mit.e...
Broad MORF_DAP3 View Gene Set 6.834e-06 175 3.602e-05 81 Neighborhood of DAP3 www.broad.mit.e...
Broad GNF2_MLH1 View Gene Set 7.403e-06 36 3.855e-05 82 Neighborhood of MLH1 www.broad.mit.e...
Broad MORF_CDK2 View Gene Set 7.666e-06 63 3.897e-05 83 Neighborhood of CDK2 www.broad.mit.e...
Broad MORF_SART1 View Gene Set 7.661e-06 55 3.897e-05 83 Neighborhood of SART1 www.broad.mit.e...
Broad MORF_MTA1 View Gene Set 8.173e-06 95 4.106e-05 85 Neighborhood of MTA1 www.broad.mit.e...
Broad MORF_CCNI View Gene Set 8.784e-06 76 4.361e-05 86 Neighborhood of CCNI www.broad.mit.e...
Broad MORF_FEN1 View Gene Set 1.301e-05 58 6.386e-05 87 Neighborhood of FEN1 www.broad.mit.e...
Broad MORF_SS18 View Gene Set 1.464e-05 55 7.105e-05 88 Neighborhood of SS18 www.broad.mit.e...
Broad MORF_RAN View Gene Set 1.91e-05 242 9.163e-05 89 Neighborhood of RAN www.broad.mit.e...
Broad MORF_CCNF View Gene Set 1.996e-05 65 9.471e-05 90 Neighborhood of CCNF www.broad.mit.e...
Broad GNF2_RPA1 View Gene Set 2.146e-05 20 0.0001007 91 Neighborhood of RPA1 www.broad.mit.e...
Broad MORF_EI24 View Gene Set 2.214e-05 136 0.0001027 92 Neighborhood of EI24 www.broad.mit.e...
Broad MORF_CUL1 View Gene Set 2.902e-05 62 0.0001333 93 Neighborhood of CUL1 www.broad.mit.e...
Broad MORF_RAD21 View Gene Set 3.239e-05 157 0.0001471 94 Neighborhood of RAD21 www.broad.mit.e...
Broad MORF_SP3 View Gene Set 3.471e-05 69 0.0001544 95 Neighborhood of SP3 www.broad.mit.e...
Broad MORF_EIF3S6 View Gene Set 3.461e-05 108 0.0001544 95 Neighborhood of EIF3S6 www.broad.mit.e...
Broad MORF_TERF2IP View Gene Set 3.714e-05 99 0.0001635 97 Neighborhood of TERF2IP www.broad.mit.e...
Broad MORF_PPP2CA View Gene Set 3.763e-05 110 0.000164 98 Neighborhood of PPP2CA www.broad.mit.e...
Broad MORF_UBE2N View Gene Set 3.822e-05 79 0.0001648 99 Neighborhood of UBE2N www.broad.mit.e...
Broad MORF_ERH View Gene Set 4.676e-05 103 0.0001997 100 Neighborhood of ERH www.broad.mit.e...
Broad MORF_PSMC1 View Gene Set 5.464e-05 162 0.000231 101 Neighborhood of PSMC1 www.broad.mit.e...
Broad GNF2_BNIP2 View Gene Set 6.323e-05 31 0.0002647 102 Neighborhood of BNIP2 www.broad.mit.e...
Broad MORF_EIF4A2 View Gene Set 7.459e-05 120 0.0003092 103 Neighborhood of EIF4A2 www.broad.mit.e...
Broad MORF_UNG View Gene Set 8.045e-05 65 0.0003272 104 Neighborhood of UNG www.broad.mit.e...
Broad MORF_SKP1A View Gene Set 8.009e-05 175 0.0003272 104 Neighborhood of SKP1A www.broad.mit.e...
Broad GCM_MLL View Gene Set 8.125e-05 130 0.0003273 106 Neighborhood of MLL www.broad.mit.e...
Broad MORF_BMI1 View Gene Set 8.404e-05 71 0.0003354 107 Neighborhood of BMI1 www.broad.mit.e...
Broad GCM_DDX5 View Gene Set 0.0001247 52 0.0004929 108 Neighborhood of DDX5 www.broad.mit.e...
Broad GCM_MAX View Gene Set 0.0001722 28 0.0006748 109 Neighborhood of MAX www.broad.mit.e...
Broad MORF_MAP2K2 View Gene Set 0.0002301 123 0.0008933 110 Neighborhood of MAP2K2 www.broad.mit.e...
Broad MORF_PPP1CA View Gene Set 0.000238 145 0.0009157 111 Neighborhood of PPP1CA www.broad.mit.e...
Broad GCM_NF2 View Gene Set 0.0002545 235 0.0009704 112 Neighborhood of NF2 www.broad.mit.e...
Broad GCM_ANP32B View Gene Set 0.0002755 32 0.001041 113 Neighborhood of ANP32B www.broad.mit.e...
Broad MORF_GMPS View Gene Set 0.0002823 48 0.001048 114 Neighborhood of GMPS www.broad.mit.e...
Broad GCM_DFFA View Gene Set 0.0002816 100 0.001048 114 Neighborhood of DFFA www.broad.mit.e...
Broad MORF_NPM1 View Gene Set 0.0003268 152 0.001203 116 Neighborhood of NPM1 www.broad.mit.e...
Broad MORF_AP3D1 View Gene Set 0.0003403 119 0.001242 117 Neighborhood of AP3D1 www.broad.mit.e...
Broad MORF_RAC1 View Gene Set 0.0004263 196 0.001542 118 Neighborhood of RAC1 www.broad.mit.e...
Broad GCM_APEX1 View Gene Set 0.0004871 102 0.001748 119 Neighborhood of APEX1 www.broad.mit.e...
Broad MORF_REV3L View Gene Set 0.0005022 52 0.001787 120 Neighborhood of REV3L www.broad.mit.e...
Broad MORF_USP5 View Gene Set 0.0005265 46 0.001858 121 Neighborhood of USP5 www.broad.mit.e...
Broad GNF2_G22P1 View Gene Set 0.0005733 29 0.002007 122 Neighborhood of G22P1 www.broad.mit.e...
Broad MORF_EIF4E View Gene Set 0.0006056 76 0.002102 123 Neighborhood of EIF4E www.broad.mit.e...
Broad GCM_MYST2 View Gene Set 0.0006217 138 0.002141 124 Neighborhood of MYST2 www.broad.mit.e...
Broad MORF_DEAF1 View Gene Set 0.000639 54 0.002183 125 Neighborhood of DEAF1 www.broad.mit.e...
Broad GNF2_PPP6C View Gene Set 0.0007063 33 0.002394 126 Neighborhood of PPP6C www.broad.mit.e...
Broad GNF2_NPM1 View Gene Set 0.0007127 57 0.002396 127 Neighborhood of NPM1 www.broad.mit.e...
Broad MORF_RFC1 View Gene Set 0.0007288 98 0.002431 128 Neighborhood of RFC1 www.broad.mit.e...
Broad MORF_CDC10 View Gene Set 0.0008065 120 0.00267 129 Neighborhood of CDC10 www.broad.mit.e...
Broad GCM_NUMA1 View Gene Set 0.00104 45 0.003415 130 Neighborhood of NUMA1 www.broad.mit.e...
Broad MORF_TPR View Gene Set 0.001059 131 0.003453 131 Neighborhood of TPR www.broad.mit.e...
Broad GCM_GSPT1 View Gene Set 0.001104 129 0.003571 132 Neighborhood of GSPT1 www.broad.mit.e...
Broad GCM_HBP1 View Gene Set 0.001116 54 0.003583 133 Neighborhood of HBP1 www.broad.mit.e...
Broad GNF2_DAP3 View Gene Set 0.001212 98 0.003861 134 Neighborhood of DAP3 www.broad.mit.e...
Broad MORF_HEAB View Gene Set 0.001277 71 0.004038 135 Neighborhood of HEAB www.broad.mit.e...
Broad GCM_SMARCC1 View Gene Set 0.001405 33 0.004413 136 Neighborhood of SMARCC1 www.broad.mit.e...
Broad MORF_AP2M1 View Gene Set 0.001574 197 0.004905 137 Neighborhood of AP2M1 www.broad.mit.e...
Broad GNF2_NS View Gene Set 0.001658 35 0.005129 138 Neighborhood of NS www.broad.mit.e...
Broad GCM_RAF1 View Gene Set 0.002333 34 0.007166 139 Neighborhood of RAF1 www.broad.mit.e...
Broad MORF_GSPT1 View Gene Set 0.002771 41 0.008451 140 Neighborhood of GSPT1 www.broad.mit.e...
Broad MORF_CSNK1D View Gene Set 0.003178 65 0.009626 141 Neighborhood of CSNK1D www.broad.mit.e...
Broad MORF_RPA1 View Gene Set 0.003357 55 0.0101 142 Neighborhood of RPA1 www.broad.mit.e...
Broad MORF_PPP5C View Gene Set 0.003391 81 0.01013 143 Neighborhood of PPP5C www.broad.mit.e...
Broad MORF_IKBKG View Gene Set 0.003503 119 0.01039 144 Neighborhood of IKBKG www.broad.mit.e...
Broad GCM_CHUK View Gene Set 0.003688 61 0.01086 145 Neighborhood of CHUK www.broad.mit.e...
Broad GNF2_TYK2 View Gene Set 0.003754 31 0.01098 146 Neighborhood of TYK2 www.broad.mit.e...
Broad GCM_PPP1CC View Gene Set 0.004275 47 0.01242 147 Neighborhood of PPP1CC www.broad.mit.e...
Broad MORF_RAD23B View Gene Set 0.004356 159 0.01257 148 Neighborhood of RAD23B www.broad.mit.e...
Broad GNF2_MSH6 View Gene Set 0.004457 30 0.01277 149 Neighborhood of MSH6 www.broad.mit.e...
Broad GCM_CBFB View Gene Set 0.004822 59 0.01373 150 Neighborhood of CBFB www.broad.mit.e...
Broad GNF2_DDX5 View Gene Set 0.005023 54 0.0142 151 Neighborhood of DDX5 www.broad.mit.e...
Broad MORF_PTPN11 View Gene Set 0.005529 93 0.01553 152 Neighborhood of PTPN11 www.broad.mit.e...
Broad GCM_HDAC1 View Gene Set 0.005699 30 0.0159 153 Neighborhood of HDAC1 www.broad.mit.e...
Broad GCM_RAD21 View Gene Set 0.006769 30 0.01877 154 Neighborhood of RAD21 www.broad.mit.e...
Broad GCM_AIP View Gene Set 0.007082 36 0.01951 155 Neighborhood of AIP www.broad.mit.e...
Broad GCM_DPF2 View Gene Set 0.007146 32 0.01956 156 Neighborhood of DPF2 www.broad.mit.e...
Broad MORF_NME2 View Gene Set 0.007485 145 0.02023 157 Neighborhood of NME2 www.broad.mit.e...
Broad MORF_PRKAR1A View Gene Set 0.007443 133 0.02023 157 Neighborhood of PRKAR1A www.broad.mit.e...
Broad MORF_PRDX3 View Gene Set 0.007713 79 0.02071 159 Neighborhood of PRDX3 www.broad.mit.e...
Broad GNF2_CBFB View Gene Set 0.007859 26 0.02097 160 Neighborhood of CBFB www.broad.mit.e...
Broad GCM_BECN1 View Gene Set 0.008889 59 0.02357 161 Neighborhood of BECN1 www.broad.mit.e...
Broad GCM_UBE2N View Gene Set 0.008972 125 0.02365 162 Neighborhood of UBE2N www.broad.mit.e...
Broad MORF_ORC1L View Gene Set 0.0101 61 0.02647 163 Neighborhood of ORC1L www.broad.mit.e...
Broad MORF_BAG5 View Gene Set 0.01025 48 0.0267 164 Neighborhood of BAG5 www.broad.mit.e...
Broad MORF_ACTG1 View Gene Set 0.01083 134 0.02803 165 Neighborhood of ACTG1 www.broad.mit.e...
Broad GCM_VAV1 View Gene Set 0.01108 46 0.02849 166 Neighborhood of VAV1 www.broad.mit.e...
Broad GCM_CSNK1A1 View Gene Set 0.01136 28 0.02905 167 Neighborhood of CSNK1A1 www.broad.mit.e...
Broad MORF_BECN1 View Gene Set 0.01268 93 0.03222 168 Neighborhood of BECN1 www.broad.mit.e...
Broad MORF_RAB1A View Gene Set 0.0131 179 0.03309 169 Neighborhood of RAB1A www.broad.mit.e...
Broad GNF2_PAK2 View Gene Set 0.01339 27 0.03363 170 Neighborhood of PAK2 www.broad.mit.e...
Broad GCM_TINF2 View Gene Set 0.01354 33 0.03381 171 Neighborhood of TINF2 www.broad.mit.e...
Broad MORF_PSMC2 View Gene Set 0.01435 100 0.03563 172 Neighborhood of PSMC2 www.broad.mit.e...
Broad GCM_RBM8A View Gene Set 0.01445 64 0.03566 173 Neighborhood of RBM8A www.broad.mit.e...
Broad GCM_PFN1 View Gene Set 0.01562 47 0.03833 174 Neighborhood of PFN1 www.broad.mit.e...
Broad GNF2_SMC1L1 View Gene Set 0.01659 24 0.04049 175 Neighborhood of SMC1L1 www.broad.mit.e...
Broad GCM_ACTG1 View Gene Set 0.01681 113 0.04077 176 Neighborhood of ACTG1 www.broad.mit.e...
Broad MORF_PAPSS1 View Gene Set 0.017 98 0.04102 177 Neighborhood of PAPSS1 www.broad.mit.e...
Broad GCM_GSTA4 View Gene Set 0.01815 57 0.04354 178 Neighborhood of GSTA4 www.broad.mit.e...
Broad GNF2_BUB3 View Gene Set 0.01963 22 0.04684 179 Neighborhood of BUB3 www.broad.mit.e...

Gene Set Collection: Broad.c4.CM

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad module_252 View Gene Set 1.065e-12 224 4.837e-10 1 Genes in module_252 www.broad.mit.e...
Broad module_198 View Gene Set 3.313e-12 288 7.519e-10 2 Genes in module_198 www.broad.mit.e...
Broad module_98 View Gene Set 6.939e-11 375 1.05e-08 3 Genes in module_98 www.broad.mit.e...
Broad module_183 View Gene Set 3.428e-08 52 3.89e-06 4 Genes in module_183 www.broad.mit.e...
Broad module_54 View Gene Set 3.447e-07 242 3.13e-05 5 Genes in module_54 www.broad.mit.e...
Broad module_57 View Gene Set 2.459e-05 54 0.001595 6 Genes in module_57 www.broad.mit.e...
Broad module_397 View Gene Set 2.322e-05 114 0.001595 6 Genes in module_397 www.broad.mit.e...
Broad module_403 View Gene Set 4.451e-05 44 0.002526 8 Genes in module_403 www.broad.mit.e...
Broad module_352 View Gene Set 0.0001166 17 0.00588 9 Genes in module_352 www.broad.mit.e...
Broad module_197 View Gene Set 0.0001841 170 0.008359 10 Genes in module_197 www.broad.mit.e...
Broad module_451 View Gene Set 0.0002566 29 0.01059 11 Genes in module_451 www.broad.mit.e...
Broad module_17 View Gene Set 0.0003298 351 0.01248 12 Genes in module_17 www.broad.mit.e...
Broad module_8 View Gene Set 0.001095 403 0.03825 13 Genes in module_8 www.broad.mit.e...
Broad module_245 View Gene Set 0.001363 26 0.04419 14 Genes in module_245 www.broad.mit.e...
Broad module_320 View Gene Set 0.001569 19 0.04451 15 Genes in module_320 www.broad.mit.e...
Broad module_337 View Gene Set 0.001543 59 0.04451 15 Genes in module_337 www.broad.mit.e...
Broad module_32 View Gene Set 0.00177 227 0.046 17 Genes in module_32 www.broad.mit.e...
Broad module_158 View Gene Set 0.001824 41 0.046 17 Genes in module_158 www.broad.mit.e...

Gene Set Collection: Broad.c5.BP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS View Gene Set 3.157e-16 1197 2.604e-13 1 Genes annotated by the GO term GO:0006139. The chemical reactions and pathways involving nucleobases nucleosides nucleotides and nucleic acids. www.broad.mit.e...
Broad RNA_METABOLIC_PROCESS View Gene Set 2.369e-14 801 9.774e-12 2 Genes annotated by the GO term GO:0016070. The chemical reactions and pathways involving RNA ribonucleic acid one of the two main type of nucleic acid consisting of a long unbranched macromolecule formed from ribonucleotides joined in 3' 5'-phosphodiester linkage. www.broad.mit.e...
Broad M_PHASE_OF_MITOTIC_CELL_CYCLE View Gene Set 5.195e-11 83 1.429e-08 3 Genes annotated by the GO term GO:0000087. Progression through M phase the part of the mitotic cell cycle during which mitosis takes place. www.broad.mit.e...
Broad CELL_CYCLE_PROCESS View Gene Set 9.515e-11 187 1.963e-08 4 Genes annotated by the GO term GO:0022402. A cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. www.broad.mit.e...
Broad CHROMOSOME_ORGANIZATION_AND_BIOGENESIS View Gene Set 1.558e-10 117 2.571e-08 5 Genes annotated by the GO term GO:0051276. A process that is carried out at the cellular level that results in the formation arrangement of constituent parts or disassembly of chromosomes structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. www.broad.mit.e...
Broad M_PHASE View Gene Set 1.923e-10 111 2.645e-08 6 Genes annotated by the GO term GO:0000279. Progression through M phase the part of the cell cycle comprising nuclear division. www.broad.mit.e...
Broad MITOSIS View Gene Set 2.575e-10 81 3.035e-08 7 Genes annotated by the GO term GO:0007067. Progression through mitosis the division of the eukaryotic cell nucleus to produce two daughter nuclei that usually contain the identical chromosome complement to their mother. www.broad.mit.e...
Broad MITOTIC_CELL_CYCLE View Gene Set 1.109e-09 148 1.144e-07 8 Genes annotated by the GO term GO:0000278. Progression through the phases of the mitotic cell cycle the most common eukaryotic cell cycle which canonically comprises four successive phases called G1 S G2 and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division or G1 and G2 phases may be absent. www.broad.mit.e...
Broad BIOPOLYMER_METABOLIC_PROCESS View Gene Set 3.297e-09 1623 2.896e-07 9 Genes annotated by the GO term GO:0043283. The chemical reactions and pathways involving biopolymers long repeating chains of monomers found in nature e.g. polysaccharides and proteins. www.broad.mit.e...
Broad CELL_CYCLE_PHASE View Gene Set 3.51e-09 167 2.896e-07 9 Genes annotated by the GO term GO:0022403. A cell cycle process comprising the steps by which a cell progresses through one of the biochemical and morphological phases and events that occur during successive cell replication or nuclear replication events. www.broad.mit.e...
Broad RNA_PROCESSING View Gene Set 1.44e-08 147 1.08e-06 11 Genes annotated by the GO term GO:0006396. Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. www.broad.mit.e...
Broad TRANSCRIPTION View Gene Set 2.689e-08 738 1.849e-06 12 Genes annotated by the GO term GO:0006350. The synthesis of either RNA on a template of DNA or DNA on a template of RNA. www.broad.mit.e...
Broad REGULATION_OF_GENE_EXPRESSION View Gene Set 4.251e-08 660 2.698e-06 13 Genes annotated by the GO term GO:0010468. Any process that modulates the frequency rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. www.broad.mit.e...
Broad RNA_SPLICING View Gene Set 8.475e-08 73 4.994e-06 14 Genes annotated by the GO term GO:0008380. The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA. www.broad.mit.e...
Broad TRANSCRIPTION_DNA_DEPENDENT View Gene Set 1.303e-07 623 7.145e-06 15 Genes annotated by the GO term GO:0006351. The synthesis of RNA on a template of DNA. www.broad.mit.e...
Broad RNA_BIOSYNTHETIC_PROCESS View Gene Set 1.386e-07 625 7.145e-06 15 Genes annotated by the GO term GO:0032774. The chemical reactions and pathways resulting in the formation of RNA ribonucleic acid one of the two main type of nucleic acid consisting of a long unbranched macromolecule formed from ribonucleotides joined in 3' 5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. www.broad.mit.e...
Broad REGULATION_OF_TRANSCRIPTION View Gene Set 1.509e-07 555 7.321e-06 17 Genes annotated by the GO term GO:0045449. Any process that modulates the frequency rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA. www.broad.mit.e...
Broad REGULATION_OF_NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS View Gene Set 3.934e-07 601 1.803e-05 18 Genes annotated by the GO term GO:0019219. Any process that modulates the frequency rate or extent of the chemical reactions and pathways involving nucleobases nucleosides nucleotides and nucleic acids. www.broad.mit.e...
Broad ESTABLISHMENT_AND_OR_MAINTENANCE_OF_CHROMATIN_ARCHITECTURE View Gene Set 5.581e-07 72 2.423e-05 19 Genes annotated by the GO term GO:0006325. The specification formation and maintenance of the physical structure of eukaryotic chromatin. www.broad.mit.e...
Broad REGULATION_OF_TRANSCRIPTIONDNA_DEPENDENT View Gene Set 8.684e-07 452 3.455e-05 20 Genes annotated by the GO term GO:0006355. Any process that modulates the frequency rate or extent of DNA-dependent transcription. www.broad.mit.e...
Broad REGULATION_OF_RNA_METABOLIC_PROCESS View Gene Set 8.795e-07 457 3.455e-05 20 Genes annotated by the GO term GO:0051252. Any process that modulates the frequency rate or extent of the chemical reactions and pathways involving RNA. www.broad.mit.e...
Broad CELL_CYCLE_GO_0007049 View Gene Set 2.042e-06 304 7.657e-05 22 Genes annotated by the GO term GO:0007049. The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. www.broad.mit.e...
Broad SISTER_CHROMATID_SEGREGATION View Gene Set 2.685e-06 17 9.63e-05 23 Genes annotated by the GO term GO:0000819. The process by which sister chromatids are organized and then physically separated and apportioned to two or more sets. www.broad.mit.e...
Broad DNA_METABOLIC_PROCESS View Gene Set 2.887e-06 253 9.925e-05 24 Genes annotated by the GO term GO:0006259. The chemical reactions and pathways involving DNA deoxyribonucleic acid one of the two main types of nucleic acid consisting of a long unbranched macromolecule formed from one or more commonly two strands of linked deoxyribonucleotides. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_TRANSCRIPTION View Gene Set 4.084e-06 185 0.0001348 25 Genes annotated by the GO term GO:0016481. Any process that stops prevents or reduces the frequency rate or extent of transcription. www.broad.mit.e...
Broad MITOTIC_SISTER_CHROMATID_SEGREGATION View Gene Set 4.311e-06 16 0.0001368 26 Genes annotated by the GO term GO:0000070. The cell cycle process whereby replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome composed of two sister chromatids aligns at the cell equator paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_TRANSCRIPTION_DNA_DEPENDENT View Gene Set 5.166e-06 127 0.0001522 27 Genes annotated by the GO term GO:0045892. Any process that stops prevents or reduces the frequency rate or extent of DNA-dependent transcription. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_RNA_METABOLIC_PROCESS View Gene Set 5.166e-06 127 0.0001522 27 Genes annotated by the GO term GO:0051253. Any process that stops prevents or reduces the frequency rate or extent of the chemical reactions and pathways involving RNA. www.broad.mit.e...
Broad TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER View Gene Set 6.511e-06 449 0.0001852 29 Genes annotated by the GO term GO:0006366. The synthesis of RNA from a DNA template by RNA polymerase II (Pol II) originating at a Pol II-specific promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs). www.broad.mit.e...
Broad REGULATION_OF_CELLULAR_METABOLIC_PROCESS View Gene Set 1.556e-05 767 0.0004279 30 Genes annotated by the GO term GO:0031323. Any process that modulates the frequency rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. www.broad.mit.e...
Broad REGULATION_OF_METABOLIC_PROCESS View Gene Set 1.867e-05 779 0.0004969 31 Genes annotated by the GO term GO:0019222. Any process that modulates the frequency rate or extent of the chemical reactions and pathways within a cell or an organism. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS View Gene Set 3.617e-05 205 0.0009325 32 Genes annotated by the GO term GO:0045934. Any process that stops prevents or reduces the frequency rate or extent of the chemical reactions and pathways involving nucleobases nucleosides nucleotides and nucleic acids. www.broad.mit.e...
Broad REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER View Gene Set 4.595e-05 285 0.001149 33 Genes annotated by the GO term GO:0006357. Any process that modulates the frequency rate or extent of transcription from an RNA polymerase II promoter. www.broad.mit.e...
Broad CHROMOSOME_SEGREGATION View Gene Set 8.464e-05 31 0.002054 34 Genes annotated by the GO term GO:0007059. The process by which genetic material in the form of chromosomes is organized and then physically separated and apportioned to two or more sets. www.broad.mit.e...
Broad CHROMATIN_ASSEMBLY_OR_DISASSEMBLY View Gene Set 0.0001067 26 0.002515 35 Genes annotated by the GO term GO:0006333. The formation or destruction of chromatin structures. www.broad.mit.e...
Broad MITOTIC_SPINDLE_ORGANIZATION_AND_BIOGENESIS View Gene Set 0.000118 9 0.002705 36 Genes annotated by the GO term GO:0007052. A process that is carried out at the cellular level which results in the formation arrangement of constituent parts or disassembly of the microtubule spindle during a mitotic cell cycle. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER View Gene Set 0.0001234 83 0.002752 37 Genes annotated by the GO term GO:0000122. Any process that stops prevents or reduces the frequency rate or extent of transcription from an RNA polymerase II promoter. www.broad.mit.e...
Broad S_PHASE View Gene Set 0.0001708 14 0.003709 38 Genes annotated by the GO term GO:0051320. Progression through S phase the part of the cell cycle during which DNA synthesis takes place. www.broad.mit.e...
Broad PROTEIN_DNA_COMPLEX_ASSEMBLY View Gene Set 0.0001835 48 0.003881 39 Genes annotated by the GO term GO:0065004. The aggregation arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex. www.broad.mit.e...
Broad MRNA_SPLICE_SITE_SELECTION View Gene Set 0.0002356 6 0.004859 40 Genes annotated by the GO term GO:0006376. Selection of a splice site by components of the assembling spliceosome. www.broad.mit.e...
Broad CHROMATIN_MODIFICATION View Gene Set 0.000295 50 0.005936 41 Genes annotated by the GO term GO:0016568. The alteration of DNA or protein in chromatin which may result in changing the chromatin structure. www.broad.mit.e...
Broad RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY View Gene Set 0.0003141 74 0.00617 42 Genes annotated by the GO term GO:0022613. The cellular process by which a complex containing RNA and proteins is synthesized aggregates and bonds together. www.broad.mit.e...
Broad CHROMATIN_REMODELING View Gene Set 0.0003934 23 0.007548 43 Genes annotated by the GO term GO:0006338. Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation. www.broad.mit.e...
Broad PROTEIN_RNA_COMPLEX_ASSEMBLY View Gene Set 0.0004897 59 0.008979 44 Genes annotated by the GO term GO:0022618. The aggregation arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. www.broad.mit.e...
Broad SPINDLE_ORGANIZATION_AND_BIOGENESIS View Gene Set 0.0004856 10 0.008979 44 Genes annotated by the GO term GO:0007051. A process that is carried out at the cellular level which results in the formation arrangement of constituent parts or disassembly of the spindle the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart. www.broad.mit.e...
Broad STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY View Gene Set 0.0008581 20 0.01506 46 Genes annotated by the GO term GO:0030518. Any series of molecular signals generated as a consequence of a steroid hormone binding to its receptor. www.broad.mit.e...
Broad INTRACELLULAR_RECEPTOR_MEDIATED_SIGNALING_PATHWAY View Gene Set 0.0008581 21 0.01506 46 Genes annotated by the GO term GO:0030522. Any series of molecular signals initiated by a ligand entering the target cell where it binds to an intracellular receptor. www.broad.mit.e...
Broad REGULATION_OF_MITOSIS View Gene Set 0.001016 40 0.01746 48 Genes annotated by the GO term GO:0007088. Any process that modulates the frequency rate or extent of mitosis. www.broad.mit.e...
Broad ANDROGEN_RECEPTOR_SIGNALING_PATHWAY View Gene Set 0.001073 12 0.0178 49 Genes annotated by the GO term GO:0030521. Any series of molecular signals generated as a consequence of an androgen binding to its receptor. www.broad.mit.e...
Broad POSITIVE_REGULATION_OF_TRANSCRIPTION View Gene Set 0.001079 139 0.0178 49 Genes annotated by the GO term GO:0045941. Any process that activates or increases the frequency rate or extent of transcription. www.broad.mit.e...
Broad REGULATION_OF_GENE_EXPRESSION_EPIGENETIC View Gene Set 0.001296 30 0.02097 51 Genes annotated by the GO term GO:0040029. Any process that modulates the frequency rate or extent of gene expression; the process is mitotically or meiotically heritable or is stably self-propagated in the cytoplasm of a resting cell and does not entail a change in DNA sequence. www.broad.mit.e...
Broad MACROMOLECULAR_COMPLEX_ASSEMBLY View Gene Set 0.001374 271 0.0218 52 Genes annotated by the GO term GO:0065003. The aggregation arrangement and bonding together of a set of macromolecules to form a complex. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_METABOLIC_PROCESS View Gene Set 0.001434 255 0.02232 53 Genes annotated by the GO term GO:0009892. Any process that stops prevents or reduces the frequency rate or extent of the chemical reactions and pathways within a cell or an organism. www.broad.mit.e...
Broad DNA_PACKAGING View Gene Set 0.001463 34 0.02235 54 Genes annotated by the GO term GO:0006323. Any process by which DNA and associated proteins are formed into a compact orderly structure. www.broad.mit.e...
Broad NEGATIVE_REGULATION_OF_CELLULAR_METABOLIC_PROCESS View Gene Set 0.001553 252 0.02329 55 Genes annotated by the GO term GO:0031324. Any process that stops prevents or reduces the frequency rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. www.broad.mit.e...
Broad TRANSCRIPTION_INITIATION_FROM_RNA_POLYMERASE_II_PROMOTER View Gene Set 0.002331 29 0.03434 56 Genes annotated by the GO term GO:0006367. Processes involved in starting transcription from the RNA polymerase II promoter. www.broad.mit.e...
Broad TRANSCRIPTION_INITIATION View Gene Set 0.002593 35 0.03688 57 Genes annotated by the GO term GO:0006352. Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. www.broad.mit.e...
Broad CHROMOSOME_CONDENSATION View Gene Set 0.002565 10 0.03688 57 Genes annotated by the GO term GO:0030261. The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division or during apoptosis in eukaryotic cells. www.broad.mit.e...
Broad CELLULAR_COMPONENT_ASSEMBLY View Gene Set 0.003398 288 0.04752 59 Genes annotated by the GO term GO:0022607. A cellular process that results in the assembly of a part of the cell. www.broad.mit.e...

Gene Set Collection: Broad.c5.CC

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad NUCLEUS View Gene Set 2.938e-23 1353 6.845e-21 1 Genes annotated by the GO term GO:0005634. A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells the nucleus contains all of the cell's chromosomes except the organellar chromosomes and is the site of RNA synthesis and processing. In some species or in specialized cell types RNA metabolism or DNA replication may be absent. www.broad.mit.e...
Broad NUCLEAR_PART View Gene Set 1.987e-18 543 2.315e-16 2 Genes annotated by the GO term GO:0044428. Any constituent part of the nucleus a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. www.broad.mit.e...
Broad NUCLEAR_LUMEN View Gene Set 3.126e-10 365 2.428e-08 3 Genes annotated by the GO term GO:0031981. The volume enclosed by the nuclear inner membrane. www.broad.mit.e...
Broad INTRACELLULAR_ORGANELLE_PART View Gene Set 2.235e-09 1144 1.302e-07 4 Genes annotated by the GO term GO:0044446. A constituent part of an intracellular organelle an organized structure of distinctive morphology and function occurring within the cell. Includes constituent parts of the nucleus mitochondria plastids vacuoles vesicles ribosomes and the cytoskeleton but excludes the plasma membrane. www.broad.mit.e...
Broad ORGANELLE_PART View Gene Set 5.18e-09 1149 2.414e-07 5 Genes annotated by the GO term GO:0044422. Any constituent part of an organelle an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus mitochondria plastids vacuoles vesicles ribosomes and the cytoskeleton but excludes the plasma membrane. www.broad.mit.e...
Broad ORGANELLE_LUMEN View Gene Set 7.375e-09 434 2.455e-07 6 Genes annotated by the GO term GO:0043233. The volume enclosed by the membranes of a particular organelle e.g. endoplasmic reticulum lumen or the space between the two lipid bilayers of a double membrane surrounding an organelle e.g. nuclear membrane lumen. www.broad.mit.e...
Broad MEMBRANE_ENCLOSED_LUMEN View Gene Set 7.375e-09 434 2.455e-07 6 Genes annotated by the GO term GO:0031974. The enclosed volume within a sealed membrane or between two sealed membranes. www.broad.mit.e...
Broad NUCLEOPLASM View Gene Set 1.786e-08 266 4.623e-07 8 Genes annotated by the GO term GO:0005654. That part of the nuclear content other than the chromosomes or the nucleolus. www.broad.mit.e...
Broad RIBONUCLEOPROTEIN_COMPLEX View Gene Set 1.786e-08 129 4.623e-07 8 Genes annotated by the GO term GO:0030529. A macromolecular complex containing both protein and RNA molecules. www.broad.mit.e...
Broad MACROMOLECULAR_COMPLEX View Gene Set 2.109e-08 914 4.624e-07 10 Genes annotated by the GO term GO:0032991. A stable assembly of two or more macromolecules i.e. proteins nucleic acids carbohydrates or lipids in which the constituent parts function together. www.broad.mit.e...
Broad CHROMOSOME View Gene Set 2.183e-08 122 4.624e-07 10 Genes annotated by the GO term GO:0005694. A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. www.broad.mit.e...
Broad CHROMOSOMAL_PART View Gene Set 2.568e-08 95 4.987e-07 12 Genes annotated by the GO term GO:0044427. Any constituent part of a chromosome a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. www.broad.mit.e...
Broad CHROMOSOMEPERICENTRIC_REGION View Gene Set 1.239e-06 31 2.22e-05 13 Genes annotated by the GO term GO:0000775. The central region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes this region corresponds to a single area of the chromosome whereas in holocentric chromosomes it is evenly distributed along the chromosome. www.broad.mit.e...
Broad CHROMATIN View Gene Set 5.563e-06 35 9.259e-05 14 Genes annotated by the GO term GO:0000785. The ordered and organized complex of DNA and protein that forms the chromosome. www.broad.mit.e...
Broad KINETOCHORE View Gene Set 6.92e-06 25 0.0001075 15 Genes annotated by the GO term GO:0000776. A multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules. www.broad.mit.e...
Broad NUCLEOPLASM_PART View Gene Set 2.544e-05 202 0.0003704 16 Genes annotated by the GO term GO:0044451. Any constituent part of the nucleoplasm that part of the nuclear content other than the chromosomes or the nucleolus. www.broad.mit.e...
Broad NUCLEOLUS View Gene Set 5.161e-05 116 0.0007073 17 Genes annotated by the GO term GO:0005730. A small dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein is not bounded by a limiting membrane and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA the processing of this RNA into 5.8S 18S and 28S components of ribosomal RNA and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome. www.broad.mit.e...
Broad PROTEIN_COMPLEX View Gene Set 6.801e-05 799 0.0008804 18 Genes annotated by the GO term GO:0043234. Any protein group composed of two or more subunits which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups such as nucleic acids metal ions or carbohydrate groups. www.broad.mit.e...
Broad SPINDLE_MICROTUBULE View Gene Set 7.885e-05 15 0.0009669 19 Genes annotated by the GO term GO:0005876. Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole. www.broad.mit.e...
Broad SMALL_NUCLEAR_RIBONUCLEOPROTEIN_COMPLEX View Gene Set 0.0002233 20 0.002601 20 Genes annotated by the GO term GO:0030532. A complex composed of RNA of the small nuclear RNA (snRNA) class and protein found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain e.g. U1 snRNP or U4/U6 snRNP. Many but not all of these complexes are involved in splicing of nuclear mRNAs. www.broad.mit.e...
Broad CHROMATIN_REMODELING_COMPLEX View Gene Set 0.000317 17 0.003455 21 Genes annotated by the GO term GO:0016585. Any complex that mediates dynamic changes in eukaryotic chromatin. www.broad.mit.e...
Broad SPINDLE View Gene Set 0.0003263 37 0.003455 21 Genes annotated by the GO term GO:0005819. The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart. www.broad.mit.e...
Broad SPLICEOSOME View Gene Set 0.0004779 44 0.004841 23 Genes annotated by the GO term GO:0005681. A ribonucleoprotein complex containing RNA and small nuclear ribonucleoproteins (snRNPs) that is assembled during the splicing of messenger RNA primary transcript to excise an intron. www.broad.mit.e...
Broad NUCLEAR_CHROMOSOME View Gene Set 0.0006892 53 0.006691 24 Genes annotated by the GO term GO:0000228. A chromosome found in the nucleus of a eukaryotic cell. www.broad.mit.e...
Broad CENTROSOME View Gene Set 0.0007621 55 0.007103 25 Genes annotated by the GO term GO:0005813. A structure comprised of a core structure (in most organisms a pair of centrioles) and peripheral material from which a microtubule-based structure such as a spindle apparatus is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells though in animal cells it changes continually during the cell-division cycle. www.broad.mit.e...
Broad NON_MEMBRANE_BOUND_ORGANELLE View Gene Set 0.0008239 613 0.00711 26 Genes annotated by the GO term GO:0043228. Organized structure of distinctive morphology and function not bounded by a lipid bilayer membrane. Includes ribosomes the cytoskeleton and chromosomes. www.broad.mit.e...
Broad INTRACELLULAR_NON_MEMBRANE_BOUND_ORGANELLE View Gene Set 0.0008239 613 0.00711 26 Genes annotated by the GO term GO:0043232. Organized structure of distinctive morphology and function not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes the cytoskeleton and chromosomes. www.broad.mit.e...
Broad NUCLEAR_CHROMATIN View Gene Set 0.001064 14 0.00885 28 Genes annotated by the GO term GO:0000790. The ordered and organized complex of DNA and protein that forms the chromosome in the nucleus. www.broad.mit.e...
Broad ENVELOPE View Gene Set 0.001488 165 0.01155 29 Genes annotated by the GO term GO:0031975. A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers and may include a cell wall layer also includes the space between layers. www.broad.mit.e...
Broad ORGANELLE_ENVELOPE View Gene Set 0.001488 165 0.01155 29 Genes annotated by the GO term GO:0031967. A double membrane structure enclosing an organelle including two lipid bilayers and the region between them. In some cases an organelle envelope may have more than two membranes. www.broad.mit.e...
Broad PROTEASOME_COMPLEX View Gene Set 0.001719 23 0.01292 31 Genes annotated by the GO term GO:0000502. A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core. www.broad.mit.e...
Broad CONDENSED_CHROMOSOME View Gene Set 0.001903 32 0.01385 32 Genes annotated by the GO term GO:0000793. A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure. www.broad.mit.e...
Broad NUCLEAR_PORE View Gene Set 0.002119 29 0.01496 33 Genes annotated by the GO term GO:0005643. Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell where the inner and outer nuclear membranes are joined. www.broad.mit.e...
Broad MICROTUBULE_ORGANIZING_CENTER View Gene Set 0.002712 64 0.01859 34 Genes annotated by the GO term GO:0005815. A region in a eukaryotic cell such as a centrosome or basal body from which microtubules grow. www.broad.mit.e...
Broad NUCLEAR_ENVELOPE View Gene Set 0.0045 71 0.02996 35 Genes annotated by the GO term GO:0005635. The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space a gap of width 20-40 nm (also called the perinuclear space). www.broad.mit.e...
Broad NUCLEAR_MEMBRANE View Gene Set 0.005798 48 0.03753 36 Genes annotated by the GO term GO:0031965. Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. www.broad.mit.e...
Broad PORE_COMPLEX View Gene Set 0.006264 34 0.03945 37 Genes annotated by the GO term GO:0046930. Any small opening in a membrane that allows the passage of gases and/or liquids. www.broad.mit.e...

Gene Set Collection: Broad.c5.MF

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad RNA_BINDING View Gene Set 3.254e-08 236 6.443e-06 1 Genes annotated by the GO term GO:0003723. Interacting selectively with an RNA molecule or a portion thereof. www.broad.mit.e...
Broad DNA_BINDING View Gene Set 2.964e-08 587 6.443e-06 1 Genes annotated by the GO term GO:0003677. Interacting selectively with DNA (deoxyribonucleic acid). www.broad.mit.e...
Broad TRANSCRIPTION_ACTIVATOR_ACTIVITY View Gene Set 4.589e-07 169 4.77e-05 3 Genes annotated by the GO term GO:0016563. Any transcription regulator activity required for initiation or upregulation of transcription. www.broad.mit.e...
Broad TRANSCRIPTION_FACTOR_BINDING View Gene Set 4.819e-07 300 4.77e-05 3 Genes annotated by the GO term GO:0008134. Interacting selectively with a transcription factor any protein required to initiate or regulate transcription. www.broad.mit.e...
Broad TRANSCRIPTION_COFACTOR_ACTIVITY View Gene Set 1.574e-06 222 0.0001247 5 Genes annotated by the GO term GO:0003712. The function that links a sequence-specific transcription factor to the core RNA polymerase II complex but does not bind DNA itself. www.broad.mit.e...
Broad HORMONE_RECEPTOR_BINDING View Gene Set 2.207e-06 29 0.0001456 6 Genes annotated by the GO term GO:0051427. Interacting selectively with a receptor for hormones. www.broad.mit.e...
Broad TRANSCRIPTION_COACTIVATOR_ACTIVITY View Gene Set 2.745e-06 121 0.0001553 7 Genes annotated by the GO term GO:0003713. The function of a transcription cofactor that activates transcription from a RNA polymerase II promoter; does not bind DNA itself. www.broad.mit.e...
Broad NUCLEAR_HORMONE_RECEPTOR_BINDING View Gene Set 4.847e-06 28 0.0002399 8 Genes annotated by the GO term GO:0035257. Interacting selectively with a nuclear hormone receptor a ligand-dependent receptor found in the nucleus of the cell. www.broad.mit.e...
Broad RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_ACTIVITY View Gene Set 5.558e-06 182 0.0002446 9 Genes annotated by the GO term GO:0003702. Functions to initiate or regulate RNA polymerase II transcription. www.broad.mit.e...
Broad TRANSLATION_FACTOR_ACTIVITY_NUCLEIC_ACID_BINDING View Gene Set 5.627e-05 39 0.002228 10 Genes annotated by the GO term GO:0008135. Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome. www.broad.mit.e...
Broad STEROID_HORMONE_RECEPTOR_BINDING View Gene Set 6.244e-05 10 0.002248 11 Genes annotated by the GO term GO:0035258. Interacting selectively with a steroid hormone receptor. www.broad.mit.e...
Broad RNA_SPLICING_FACTOR_ACTIVITYTRANSESTERIFICATION_MECHANISM View Gene Set 9.978e-05 14 0.003293 12 Genes annotated by the GO term GO:0031202. An activity which binds RNA and functions to assist splicing of substrate RNA(s) by facilitating the formation and stabilization of a catalytic conformation in which the splice junctions of the RNA(s) to be spliced are positioned for a transesterification reaction that occurs between two sites within the RNA(s) to be spliced. www.broad.mit.e...
Broad TRANSLATION_REGULATOR_ACTIVITY View Gene Set 0.0001311 41 0.003993 13 Genes annotated by the GO term GO:0045182. Any substance involved in the initiation activation perpetuation repression or termination of polypeptide synthesis at the ribosome. www.broad.mit.e...
Broad CHROMATIN_BINDING View Gene Set 0.0001693 32 0.004789 14 Genes annotated by the GO term GO:0003682. Interacting selectively with chromatin the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase. www.broad.mit.e...
Broad SIGNAL_SEQUENCE_BINDING View Gene Set 0.001776 15 0.04684 15 Genes annotated by the GO term GO:0005048. Interacting selectively with a signal sequence a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized. www.broad.mit.e...
Broad TRANSLATION_INITIATION_FACTOR_ACTIVITY View Gene Set 0.001893 24 0.04684 15 Genes annotated by the GO term GO:0003743. Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide. www.broad.mit.e...

Gene Set Collection: PMID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
PMID 15302935 View Gene Set 8.438e-26 773 2.115e-22 1 Large-scale characterization of HeLa cell nuclear phosphoproteins. www.ncbi.nlm.ni...
PMID 16964243 View Gene Set 7.02e-16 504 6.933e-13 2 A probability-based approach for high-throughput protein phosphorylation analysis and site localization. www.ncbi.nlm.ni...
PMID 17643375 View Gene Set 8.297e-16 391 6.933e-13 2 Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. www.ncbi.nlm.ni...
PMID 12226669 View Gene Set 9.754e-12 108 6.114e-09 4 Comprehensive proteomic analysis of the human spliceosome. www.ncbi.nlm.ni...
PMID 15635413 View Gene Set 7.822e-11 421 3.922e-08 5 Nucleolar proteome dynamics. www.ncbi.nlm.ni...
PMID 11991638 View Gene Set 1.607e-10 74 6.715e-08 6 Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. www.ncbi.nlm.ni...
PMID 11790298 View Gene Set 2.249e-09 208 7.392e-07 7 Directed proteomic analysis of the human nucleolus. www.ncbi.nlm.ni...
PMID 14559993 View Gene Set 2.359e-09 51 7.392e-07 7 Regulation of alternative splicing by SRrp86 and its interacting proteins. www.ncbi.nlm.ni...
PMID 16565220 View Gene Set 7.696e-09 210 2.144e-06 9 Phosphoproteome analysis of the human mitotic spindle. www.ncbi.nlm.ni...
PMID 9731529 View Gene Set 7.212e-08 24 1.808e-05 10 Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. www.ncbi.nlm.ni...
PMID 12429849 View Gene Set 5.146e-07 106 0.0001173 11 Functional proteomic analysis of human nucleolus. www.ncbi.nlm.ni...
PMID 12837248 View Gene Set 9.857e-07 22 0.0002059 12 The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome. www.ncbi.nlm.ni...
PMID 16387653 View Gene Set 2.203e-06 42 0.0004249 13 ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. www.ncbi.nlm.ni...
PMID 11500380 View Gene Set 2.383e-06 10 0.0004267 14 A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. www.ncbi.nlm.ni...
PMID 20085707 View Gene Set 2.64e-06 42 0.0004413 15 Aire's partners in the molecular control of immunological tolerance. www.ncbi.nlm.ni...
PMID 8724849 View Gene Set 4.698e-06 41 0.0007362 16 Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1. www.ncbi.nlm.ni...
PMID 11076961 View Gene Set 5.868e-06 14 0.0008654 17 Characterization of vertebrate cohesin complexes and their regulation in prophase. www.ncbi.nlm.ni...
PMID 12234937 View Gene Set 8.091e-06 34 0.001127 18 Characterization of novel SF3b and 17S U2 snRNP proteins including a human Prp5p homologue and an SF3b DEAD-box protein. www.ncbi.nlm.ni...
PMID 11078522 View Gene Set 1.075e-05 12 0.001418 19 The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. www.ncbi.nlm.ni...
PMID 11780052 View Gene Set 1.163e-05 517 0.001458 20 The DNA sequence and comparative analysis of human chromosome 20. www.ncbi.nlm.ni...
PMID 17148452 View Gene Set 1.451e-05 87 0.001706 21 Characterization of the interactome of the human MutL homologues MLH1 PMS1 and PMS2. www.ncbi.nlm.ni...
PMID 20516191 View Gene Set 1.497e-05 12 0.001706 21 A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins). www.ncbi.nlm.ni...
PMID 8895581 View Gene Set 1.957e-05 12 0.002133 23 Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. www.ncbi.nlm.ni...
PMID 15504738 View Gene Set 3.364e-05 19 0.003514 24 Genes affecting the cell cycle growth maintenance and drug sensitivity are preferentially regulated by anti-HER2 antibody through phosphatidylinositol 3-kinase-AKT signaling. www.ncbi.nlm.ni...
PMID 19710015 View Gene Set 4.098e-05 48 0.004109 25 The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor. www.ncbi.nlm.ni...
PMID 12706105 View Gene Set 4.76e-05 182 0.00459 26 Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome. www.ncbi.nlm.ni...
PMID 12388589 View Gene Set 6.893e-05 17 0.0064 27 A receptor for activated C kinase is part of messenger ribonucleoprotein complexes associated with polyA-mRNAs in neurons. www.ncbi.nlm.ni...
PMID 18162579 View Gene Set 9.463e-05 22 0.0082 28 Identification of novel human Cdt1-binding proteins by a proteomics approach: proteolytic regulation by APC/CCdh1. www.ncbi.nlm.ni...
PMID 20508983 View Gene Set 9.486e-05 102 0.0082 28 Centrosome-related genes genetic variation and risk of breast cancer. www.ncbi.nlm.ni...
PMID 10078207 View Gene Set 0.0001791 10 0.01497 30 Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. www.ncbi.nlm.ni...
PMID 11734557 View Gene Set 0.0001895 12 0.01533 31 SYT associates with human SNF/SWI complexes and the C-terminal region of its fusion partner SSX1 targets histones. www.ncbi.nlm.ni...
PMID 15146077 View Gene Set 0.0002033 32 0.01545 32 The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. www.ncbi.nlm.ni...
PMID 9472028 View Gene Set 0.000199 12 0.01545 32 SRPK2: a differentially expressed SR protein-specific kinase involved in mediating the interaction and localization of pre-mRNA splicing factors in mammalian cells. www.ncbi.nlm.ni...
PMID 11018012 View Gene Set 0.0002225 11 0.01594 34 Functional selectivity of recombinant mammalian SWI/SNF subunits. www.ncbi.nlm.ni...
PMID 19138993 View Gene Set 0.0002164 25 0.01594 34 Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. www.ncbi.nlm.ni...
PMID 15456888 View Gene Set 0.0002408 24 0.01655 36 The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. www.ncbi.nlm.ni...
PMID 19047128 View Gene Set 0.0002443 19 0.01655 36 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. www.ncbi.nlm.ni...
PMID 14966270 View Gene Set 0.0002513 19 0.01658 38 Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. www.ncbi.nlm.ni...
PMID 10983978 View Gene Set 0.0003361 10 0.02055 39 Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. www.ncbi.nlm.ni...
PMID 18485873 View Gene Set 0.0003349 13 0.02055 39 Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. www.ncbi.nlm.ni...
PMID 18997788 View Gene Set 0.000326 10 0.02055 39 The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction. www.ncbi.nlm.ni...
PMID 11101529 View Gene Set 0.0004084 34 0.02437 42 Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry. www.ncbi.nlm.ni...
PMID 17363900 View Gene Set 0.0004269 14 0.02489 43 The human Nup107-160 nuclear pore subcomplex contributes to proper kinetochore functions. www.ncbi.nlm.ni...
PMID 15647280 View Gene Set 0.0004423 17 0.0252 44 The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. www.ncbi.nlm.ni...
PMID 15502821 View Gene Set 0.0004559 12 0.0254 45 A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1. www.ncbi.nlm.ni...
PMID 19690177 View Gene Set 0.0004977 31 0.02712 46 Polymorphic variants in hereditary pancreatic cancer genes are not associated with pancreatic cancer risk. www.ncbi.nlm.ni...
PMID 14729942 View Gene Set 0.0005705 18 0.03043 47 Identification of phosphoproteins and their phosphorylation sites in the WEHI-231 B lymphoma cell line. www.ncbi.nlm.ni...
PMID 17289661 View Gene Set 0.0005932 35 0.03098 48 Molecular composition of IMP1 ribonucleoprotein granules. www.ncbi.nlm.ni...
PMID 18377426 View Gene Set 0.0006717 20 0.03437 49 Interaction of antiproliferative protein Tob with the CCR4-NOT deadenylase complex. www.ncbi.nlm.ni...
PMID 1358459 View Gene Set 0.0007486 40 0.0368 50 Vertebrate homeobox gene nomenclature. www.ncbi.nlm.ni...
PMID 14578343 View Gene Set 0.0007456 19 0.0368 50 Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. www.ncbi.nlm.ni...
PMID 20496165 View Gene Set 0.0007804 68 0.03691 52 Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. www.ncbi.nlm.ni...
PMID 9153318 View Gene Set 0.0007708 11 0.03691 52 CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues. www.ncbi.nlm.ni...
PMID 15009096 View Gene Set 0.0009224 39 0.04283 54 Proteomics analysis of the centromere complex from HeLa interphase cells: UV-damaged DNA binding protein 1 (DDB-1) is a component of the CEN-complex while BMI-1 is transiently co-localized with the centromeric region in interphase. www.ncbi.nlm.ni...
PMID 11416179 View Gene Set 0.0009818 12 0.04408 55 All kinesin superfamily protein KIF genes in mouse and human. www.ncbi.nlm.ni...
PMID 16364912 View Gene Set 0.0009847 12 0.04408 55 Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C. www.ncbi.nlm.ni...
PMID 11535616 View Gene Set 0.001055 18 0.04482 57 Checkpoint inhibition of the APC/C in HeLa cells is mediated by a complex of BUBR1 BUB3 CDC20 and MAD2. www.ncbi.nlm.ni...
PMID 14593737 View Gene Set 0.001055 18 0.04482 57 The mitotic checkpoint: a signaling pathway that allows a single unattached kinetochore to inhibit mitotic exit. www.ncbi.nlm.ni...
PMID 15231747 View Gene Set 0.001024 212 0.04482 57 A protein interaction framework for human mRNA degradation. www.ncbi.nlm.ni...
PMID 11279123 View Gene Set 0.001109 31 0.04633 60 The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. www.ncbi.nlm.ni...

Gene Set Collection: Prosite

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null PS50102 View Gene Set 2.478e-23 229 1.822e-20 1 RRM expasy.org/pros...
Null PS50157 View Gene Set 3.028e-13 811 1.113e-10 2 ZINC_FINGER_C2H2_2 expasy.org/pros...
Null PS00028 View Gene Set 7.035e-13 830 1.724e-10 3 ZINC_FINGER_C2H2_1 expasy.org/pros...
Null PS50014 View Gene Set 9.881e-07 41 0.0001816 4 BROMODOMAIN_2 expasy.org/pros...
Null PS50805 View Gene Set 3.62e-06 415 0.0005322 5 KRAB expasy.org/pros...
Null PS00633 View Gene Set 1.927e-05 26 0.00236 6 BROMODOMAIN_1 expasy.org/pros...
Null PS50868 View Gene Set 4.02e-05 16 0.004221 7 POST_SET expasy.org/pros...
Null PS50280 View Gene Set 0.000109 47 0.01001 8 SET expasy.org/pros...
Null PS50051 View Gene Set 0.0002051 8 0.01675 9 MCM_2 expasy.org/pros...
Null PS50016 View Gene Set 0.0002418 78 0.01777 10 ZF_PHD_2 expasy.org/pros...
Null PS01359 View Gene Set 0.0003641 72 0.02253 11 ZF_PHD_1 expasy.org/pros...
Null PS50166 View Gene Set 0.0003678 13 0.02253 11 IMPORTIN_B_NT expasy.org/pros...
Null PS50118 View Gene Set 0.0004076 63 0.02304 13 HMG_BOX_2 expasy.org/pros...
Null PS50800 View Gene Set 0.0004915 23 0.02505 14 SAP expasy.org/pros...
Null PS50867 View Gene Set 0.0005112 7 0.02505 14 PRE_SET expasy.org/pros...
Null PS00847 View Gene Set 0.0007439 6 0.03417 16 MCM_1 expasy.org/pros...

Gene Set Collection: Enzyme

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null EC:2.1.1.43 View Gene Set 3.981e-06 19 0.000629 1 Histone-lysine N-methyltransferase expasy.org/enzy...

Gene Set Collection: ppi.BIND

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null ppi.RBL2 View Gene Set 0.0007312 14 0.04607 1 Protein-protein-interaction for RBL2 www.ncbi.nlm.ni...
Null ppi.TFF1 View Gene Set 0.0003967 8 0.04607 1 Protein-protein-interaction for TFF1 www.ncbi.nlm.ni...
Null ppi.CFLAR View Gene Set 0.0005413 6 0.04607 1 Protein-protein-interaction for CFLAR www.ncbi.nlm.ni...

Gene Set Collection: ppi.BioGRID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null ppi.155871 View Gene Set 7.673e-14 236 1.763e-10 1 Protein-protein-interaction for 155871 www.ncbi.nlm.ni...
Null ppi.MEPCE View Gene Set 5.37e-11 147 6.168e-08 2 Protein-protein-interaction for MEPCE www.ncbi.nlm.ni...
Null ppi.WBP4 View Gene Set 5.266e-10 35 4.032e-07 3 Protein-protein-interaction for WBP4 www.ncbi.nlm.ni...
Null ppi.SRRM1 View Gene Set 3.825e-09 64 2.197e-06 4 Protein-protein-interaction for SRRM1 www.ncbi.nlm.ni...
Null ppi.PRPF40A View Gene Set 4.657e-08 53 2.139e-05 5 Protein-protein-interaction for PRPF40A www.ncbi.nlm.ni...
Null ppi.SRRM2 View Gene Set 2.631e-07 101 0.0001007 6 Protein-protein-interaction for SRRM2 www.ncbi.nlm.ni...
Null ppi.ING5 View Gene Set 5.976e-07 20 0.0001961 7 Protein-protein-interaction for ING5 www.ncbi.nlm.ni...
Null ppi.HIST1H4A View Gene Set 1.414e-06 28 0.000406 8 Protein-protein-interaction for HIST1H4A www.ncbi.nlm.ni...
Null ppi.KLF1 View Gene Set 5.091e-06 13 0.001299 9 Protein-protein-interaction for KLF1 www.ncbi.nlm.ni...
Null ppi.BCL7C View Gene Set 7.068e-06 11 0.001624 10 Protein-protein-interaction for BCL7C www.ncbi.nlm.ni...
Null ppi.CBX5 View Gene Set 1.047e-05 38 0.002185 11 Protein-protein-interaction for CBX5 www.ncbi.nlm.ni...
Null ppi.72462 View Gene Set 1.908e-05 42 0.003652 12 Protein-protein-interaction for 72462 www.ncbi.nlm.ni...
Null ppi.TAF6 View Gene Set 4.2e-05 19 0.007421 13 Protein-protein-interaction for TAF6 www.ncbi.nlm.ni...
Null ppi.TCERG1 View Gene Set 5.113e-05 35 0.00839 14 Protein-protein-interaction for TCERG1 www.ncbi.nlm.ni...
Null ppi.CBX3 View Gene Set 6.867e-05 23 0.01052 15 Protein-protein-interaction for CBX3 www.ncbi.nlm.ni...
Null ppi.CARM1 View Gene Set 7.91e-05 32 0.01136 16 Protein-protein-interaction for CARM1 www.ncbi.nlm.ni...
Null ppi.CHEK2 View Gene Set 8.418e-05 19 0.01137 17 Protein-protein-interaction for CHEK2 www.ncbi.nlm.ni...
Null ppi.THRA View Gene Set 0.0001331 16 0.01698 18 Protein-protein-interaction for THRA www.ncbi.nlm.ni...
Null ppi.SF3B2 View Gene Set 0.0001554 11 0.01879 19 Protein-protein-interaction for SF3B2 www.ncbi.nlm.ni...
Null ppi.SSRP1 View Gene Set 0.000176 15 0.02022 20 Protein-protein-interaction for SSRP1 www.ncbi.nlm.ni...
Null ppi.MDM4 View Gene Set 0.0002349 10 0.0214 21 Protein-protein-interaction for MDM4 www.ncbi.nlm.ni...
Null ppi.SP1 View Gene Set 0.0002205 79 0.0214 21 Protein-protein-interaction for SP1 www.ncbi.nlm.ni...
Null ppi.ZEB1 View Gene Set 0.0002188 6 0.0214 21 Protein-protein-interaction for ZEB1 www.ncbi.nlm.ni...
Null ppi.MCPH1 View Gene Set 0.0002283 17 0.0214 21 Protein-protein-interaction for MCPH1 www.ncbi.nlm.ni...
Null ppi.HIST1H3A View Gene Set 0.0002196 30 0.0214 21 Protein-protein-interaction for HIST1H3A www.ncbi.nlm.ni...
Null ppi.CDC16 View Gene Set 0.0002422 10 0.0214 21 Protein-protein-interaction for CDC16 www.ncbi.nlm.ni...
Null ppi.NCOA6 View Gene Set 0.0002746 48 0.02227 27 Protein-protein-interaction for NCOA6 www.ncbi.nlm.ni...
Null ppi.CDC7 View Gene Set 0.0002731 7 0.02227 27 Protein-protein-interaction for CDC7 www.ncbi.nlm.ni...
Null ppi.HIST2H2AC View Gene Set 0.0002812 13 0.02227 27 Protein-protein-interaction for HIST2H2AC www.ncbi.nlm.ni...
Null ppi.855836 View Gene Set 0.000375 8 0.02871 30 Protein-protein-interaction for 855836 www.ncbi.nlm.ni...
Null ppi.WWOX View Gene Set 0.0004253 19 0.03151 31 Protein-protein-interaction for WWOX www.ncbi.nlm.ni...
Null ppi.MDC1 View Gene Set 0.0004532 20 0.03253 32 Protein-protein-interaction for MDC1 www.ncbi.nlm.ni...
Null ppi.IMMT View Gene Set 0.0005355 15 0.03727 33 Protein-protein-interaction for IMMT www.ncbi.nlm.ni...
Null ppi.RELB View Gene Set 0.0005579 10 0.03769 34 Protein-protein-interaction for RELB www.ncbi.nlm.ni...
Null ppi.U2AF2 View Gene Set 0.0006538 14 0.03998 35 Protein-protein-interaction for U2AF2 www.ncbi.nlm.ni...
Null ppi.HSPA8 View Gene Set 0.000643 21 0.03998 35 Protein-protein-interaction for HSPA8 www.ncbi.nlm.ni...
Null ppi.PIAS4 View Gene Set 0.0006762 22 0.03998 35 Protein-protein-interaction for PIAS4 www.ncbi.nlm.ni...
Null ppi.ING3 View Gene Set 0.000731 10 0.03998 35 Protein-protein-interaction for ING3 www.ncbi.nlm.ni...
Null ppi.PSMD10 View Gene Set 0.0006432 14 0.03998 35 Protein-protein-interaction for PSMD10 www.ncbi.nlm.ni...
Null ppi.TP53BP1 View Gene Set 0.0007278 13 0.03998 35 Protein-protein-interaction for TP53BP1 www.ncbi.nlm.ni...
Null ppi.MIS12 View Gene Set 0.0007115 9 0.03998 35 Protein-protein-interaction for MIS12 www.ncbi.nlm.ni...
Null ppi.NUP153 View Gene Set 0.0007279 11 0.03998 35 Protein-protein-interaction for NUP153 www.ncbi.nlm.ni...
Null ppi.UCHL5 View Gene Set 0.000749 33 0.04001 43 Protein-protein-interaction for UCHL5 www.ncbi.nlm.ni...
Null ppi.SF3B3 View Gene Set 0.0008553 16 0.04465 44 Protein-protein-interaction for SF3B3 www.ncbi.nlm.ni...
Null ppi.SF3A3 View Gene Set 0.0009035 7 0.04612 45 Protein-protein-interaction for SF3A3 www.ncbi.nlm.ni...
Null ppi.RNPS1 View Gene Set 0.000996 38 0.04868 46 Protein-protein-interaction for RNPS1 www.ncbi.nlm.ni...
Null ppi.DEK View Gene Set 0.0009911 8 0.04868 46 Protein-protein-interaction for DEK www.ncbi.nlm.ni...

Gene Set Collection: ppi.HPRD

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null ppi.SFRS12 View Gene Set 2.142e-09 49 5.084e-06 1 Protein-protein-interaction for SFRS12 www.ncbi.nlm.ni...
Null ppi.MDC1 View Gene Set 2.767e-05 11 0.03284 2 Protein-protein-interaction for MDC1 www.ncbi.nlm.ni...
Null ppi.PARP2 View Gene Set 6.668e-05 7 0.03639 3 Protein-protein-interaction for PARP2 www.ncbi.nlm.ni...
Null ppi.NCOA6 View Gene Set 9.002e-05 36 0.03639 3 Protein-protein-interaction for NCOA6 www.ncbi.nlm.ni...
Null ppi.RAN View Gene Set 5.844e-05 14 0.03639 3 Protein-protein-interaction for RAN www.ncbi.nlm.ni...
Null ppi.RFX1 View Gene Set 0.0001065 11 0.03639 3 Protein-protein-interaction for RFX1 www.ncbi.nlm.ni...
Null ppi.TAF10 View Gene Set 0.0001073 13 0.03639 3 Protein-protein-interaction for TAF10 www.ncbi.nlm.ni...
Null ppi.PRPF40A View Gene Set 0.000138 55 0.04094 8 Protein-protein-interaction for PRPF40A www.ncbi.nlm.ni...
Null ppi.TAF11 View Gene Set 0.0001625 12 0.04286 9 Protein-protein-interaction for TAF11 www.ncbi.nlm.ni...
Null ppi.TAF1 View Gene Set 0.0002048 16 0.04863 10 Protein-protein-interaction for TAF1 www.ncbi.nlm.ni...
Null ppi.SF3B1 View Gene Set 0.0002478 9 0.04902 11 Protein-protein-interaction for SF3B1 www.ncbi.nlm.ni...
Null ppi.ZEB1 View Gene Set 0.0002275 6 0.04902 11 Protein-protein-interaction for ZEB1 www.ncbi.nlm.ni...

Gene Set Collection: ppi.anyDB

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null ppi.155871 View Gene Set 6.217e-14 251 2.235e-10 1 Protein-protein-interaction for 155871 www.ncbi.nlm.ni...
Null ppi.MEPCE View Gene Set 5.37e-11 147 9.651e-08 2 Protein-protein-interaction for MEPCE www.ncbi.nlm.ni...
Null ppi.WBP4 View Gene Set 5.266e-10 35 6.309e-07 3 Protein-protein-interaction for WBP4 www.ncbi.nlm.ni...
Null ppi.SFRS12 View Gene Set 8.167e-10 50 7.338e-07 4 Protein-protein-interaction for SFRS12 www.ncbi.nlm.ni...
Null ppi.SRRM1 View Gene Set 9.405e-09 66 6.761e-06 5 Protein-protein-interaction for SRRM1 www.ncbi.nlm.ni...
Null ppi.PRPF40A View Gene Set 2.377e-08 96 1.424e-05 6 Protein-protein-interaction for PRPF40A www.ncbi.nlm.ni...
Null ppi.SRRM2 View Gene Set 2.631e-07 101 0.0001351 7 Protein-protein-interaction for SRRM2 www.ncbi.nlm.ni...
Null ppi.HIST1H4A View Gene Set 1.316e-06 31 0.0005914 8 Protein-protein-interaction for HIST1H4A www.ncbi.nlm.ni...
Null ppi.CBX5 View Gene Set 7.555e-06 46 0.002715 9 Protein-protein-interaction for CBX5 www.ncbi.nlm.ni...
Null ppi.BCL7C View Gene Set 7.068e-06 11 0.002715 9 Protein-protein-interaction for BCL7C www.ncbi.nlm.ni...
Null ppi.TAF11 View Gene Set 1.556e-05 19 0.004659 11 Protein-protein-interaction for TAF11 www.ncbi.nlm.ni...
Null ppi.ING5 View Gene Set 1.507e-05 25 0.004659 11 Protein-protein-interaction for ING5 www.ncbi.nlm.ni...
Null ppi.SSRP1 View Gene Set 1.986e-05 21 0.005098 13 Protein-protein-interaction for SSRP1 www.ncbi.nlm.ni...
Null ppi.72462 View Gene Set 1.908e-05 42 0.005098 13 Protein-protein-interaction for 72462 www.ncbi.nlm.ni...
Null ppi.MDC1 View Gene Set 2.791e-05 24 0.006687 15 Protein-protein-interaction for MDC1 www.ncbi.nlm.ni...
Null ppi.RAN View Gene Set 3.018e-05 15 0.00678 16 Protein-protein-interaction for RAN www.ncbi.nlm.ni...
Null ppi.KLF1 View Gene Set 4.226e-05 14 0.008437 17 Protein-protein-interaction for KLF1 www.ncbi.nlm.ni...
Null ppi.SF3B2 View Gene Set 4.043e-05 12 0.008437 17 Protein-protein-interaction for SF3B2 www.ncbi.nlm.ni...
Null ppi.PIAS4 View Gene Set 5.294e-05 47 0.01001 19 Protein-protein-interaction for PIAS4 www.ncbi.nlm.ni...
Null ppi.CARM1 View Gene Set 6.069e-05 35 0.01091 20 Protein-protein-interaction for CARM1 www.ncbi.nlm.ni...
Null ppi.TCERG1 View Gene Set 6.635e-05 39 0.01136 21 Protein-protein-interaction for TCERG1 www.ncbi.nlm.ni...
Null ppi.TAF6 View Gene Set 7.223e-05 23 0.0118 22 Protein-protein-interaction for TAF6 www.ncbi.nlm.ni...
Null ppi.CBX3 View Gene Set 8.046e-05 26 0.01257 23 Protein-protein-interaction for CBX3 www.ncbi.nlm.ni...
Null ppi.PBRM1 View Gene Set 8.49e-05 7 0.01271 24 Protein-protein-interaction for PBRM1 www.ncbi.nlm.ni...
Null ppi.NCOA6 View Gene Set 9.706e-05 61 0.01395 25 Protein-protein-interaction for NCOA6 www.ncbi.nlm.ni...
Null ppi.SP1 View Gene Set 0.0001099 104 0.0152 26 Protein-protein-interaction for SP1 www.ncbi.nlm.ni...
Null ppi.TPX2 View Gene Set 0.0001363 5 0.01758 27 Protein-protein-interaction for TPX2 www.ncbi.nlm.ni...
Null ppi.HIST2H2AC View Gene Set 0.000137 14 0.01758 27 Protein-protein-interaction for HIST2H2AC www.ncbi.nlm.ni...
Null ppi.TP53BP1 View Gene Set 0.000153 17 0.01896 29 Protein-protein-interaction for TP53BP1 www.ncbi.nlm.ni...
Null ppi.RFX1 View Gene Set 0.0001692 12 0.02027 30 Protein-protein-interaction for RFX1 www.ncbi.nlm.ni...
Null ppi.TFF1 View Gene Set 0.0001819 9 0.02109 31 Protein-protein-interaction for TFF1 www.ncbi.nlm.ni...
Null ppi.CHEK2 View Gene Set 0.000196 33 0.02201 32 Protein-protein-interaction for CHEK2 www.ncbi.nlm.ni...
Null ppi.XRN1 View Gene Set 0.0002275 25 0.02279 33 Protein-protein-interaction for XRN1 www.ncbi.nlm.ni...
Null ppi.XPO1 View Gene Set 0.0002209 43 0.02279 33 Protein-protein-interaction for XPO1 www.ncbi.nlm.ni...
Null ppi.MCPH1 View Gene Set 0.0002283 17 0.02279 33 Protein-protein-interaction for MCPH1 www.ncbi.nlm.ni...
Null ppi.HIST1H3A View Gene Set 0.000218 31 0.02279 33 Protein-protein-interaction for HIST1H3A www.ncbi.nlm.ni...
Null ppi.SAFB View Gene Set 0.0002834 9 0.0268 37 Protein-protein-interaction for SAFB www.ncbi.nlm.ni...
Null ppi.YY1 View Gene Set 0.0002774 39 0.0268 37 Protein-protein-interaction for YY1 www.ncbi.nlm.ni...
Null ppi.TGS1 View Gene Set 0.0003094 8 0.02851 39 Protein-protein-interaction for TGS1 www.ncbi.nlm.ni...
Null ppi.SF3A3 View Gene Set 0.0003282 8 0.02949 40 Protein-protein-interaction for SF3A3 www.ncbi.nlm.ni...
Null ppi.PARP2 View Gene Set 0.0003619 10 0.03172 41 Protein-protein-interaction for PARP2 www.ncbi.nlm.ni...
Null ppi.855836 View Gene Set 0.000375 8 0.03209 42 Protein-protein-interaction for 855836 www.ncbi.nlm.ni...
Null ppi.ING3 View Gene Set 0.0004036 12 0.03373 43 Protein-protein-interaction for ING3 www.ncbi.nlm.ni...
Null ppi.SF3B3 View Gene Set 0.0004141 19 0.03382 44 Protein-protein-interaction for SF3B3 www.ncbi.nlm.ni...
Null ppi.RYBP View Gene Set 0.0004509 15 0.03509 45 Protein-protein-interaction for RYBP www.ncbi.nlm.ni...
Null ppi.SF3B1 View Gene Set 0.0004573 31 0.03509 45 Protein-protein-interaction for SF3B1 www.ncbi.nlm.ni...
Null ppi.EAPP View Gene Set 0.0004606 6 0.03509 45 Protein-protein-interaction for EAPP www.ncbi.nlm.ni...
Null ppi.TAF10 View Gene Set 0.0004784 29 0.03509 45 Protein-protein-interaction for TAF10 www.ncbi.nlm.ni...
Null ppi.CDC16 View Gene Set 0.0004724 14 0.03509 45 Protein-protein-interaction for CDC16 www.ncbi.nlm.ni...
Null ppi.PSMD10 View Gene Set 0.000533 16 0.03756 50 Protein-protein-interaction for PSMD10 www.ncbi.nlm.ni...
Null ppi.TAF1 View Gene Set 0.0005311 24 0.03756 50 Protein-protein-interaction for TAF1 www.ncbi.nlm.ni...
Null ppi.RELB View Gene Set 0.0005579 10 0.03783 52 Protein-protein-interaction for RELB www.ncbi.nlm.ni...
Null ppi.KAT2B View Gene Set 0.0005551 88 0.03783 52 Protein-protein-interaction for KAT2B www.ncbi.nlm.ni...
Null ppi.XPO5 View Gene Set 0.0005742 14 0.03822 54 Protein-protein-interaction for XPO5 www.ncbi.nlm.ni...
Null ppi.ITGB3BP View Gene Set 0.0006731 13 0.0405 55 Protein-protein-interaction for ITGB3BP www.ncbi.nlm.ni...
Null ppi.ATXN3 View Gene Set 0.0006686 7 0.0405 55 Protein-protein-interaction for ATXN3 www.ncbi.nlm.ni...
Null ppi.PTMA View Gene Set 0.0006312 21 0.0405 55 Protein-protein-interaction for PTMA www.ncbi.nlm.ni...
Null ppi.RAD51 View Gene Set 0.0006762 20 0.0405 55 Protein-protein-interaction for RAD51 www.ncbi.nlm.ni...
Null ppi.ATXN7 View Gene Set 0.0006213 11 0.0405 55 Protein-protein-interaction for ATXN7 www.ncbi.nlm.ni...
Null ppi.NUP153 View Gene Set 0.0006722 16 0.0405 55 Protein-protein-interaction for NUP153 www.ncbi.nlm.ni...
Null ppi.MIS12 View Gene Set 0.0007115 9 0.04192 61 Protein-protein-interaction for MIS12 www.ncbi.nlm.ni...

Gene Set Collection: pathwayCommons.cell-map

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null AndrogenReceptor View Gene Set 4.517e-05 78 0.0004517 1 CELL_MAP - AndrogenReceptor gene set www.pathwaycomm...
Null TNF alpha/NF-kB View Gene Set 0.009242 170 0.04621 2 CELL_MAP - TNF alpha/NF-kB gene set www.pathwaycomm...

Gene Set Collection: pathwayCommons.nci-nature

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null Aurora B signaling View Gene Set 2.185e-05 41 0.004065 1 NCI_NATURE - Aurora B signaling gene set www.pathwaycomm...
Null C-MYC pathway View Gene Set 0.0001203 149 0.01119 2 NCI_NATURE - C-MYC pathway gene set www.pathwaycomm...
Null Regulation of retinoblastoma protein View Gene Set 0.0004418 66 0.02739 3 NCI_NATURE - Regulation of retinoblastoma protein gene set www.pathwaycomm...

Gene Set Collection: pathwayCommons.reactome

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null Processing of Capped Intron-Containing Pre-mRNA View Gene Set 4.974e-12 138 5.556e-09 1 REACTOME - Processing of Capped Intron-Containing Pre-mRNA gene set www.pathwaycomm...
Null mRNA Splicing - Major Pathway View Gene Set 2.468e-11 107 9.19e-09 2 REACTOME - mRNA Splicing - Major Pathway gene set www.pathwaycomm...
Null mRNA Splicing View Gene Set 2.468e-11 107 9.19e-09 2 REACTOME - mRNA Splicing gene set www.pathwaycomm...
Null Gene Expression View Gene Set 5.486e-11 381 1.532e-08 4 REACTOME - Gene Expression gene set www.pathwaycomm...
Null Formation and Maturation of mRNA Transcript View Gene Set 7.376e-11 185 1.648e-08 5 REACTOME - Formation and Maturation of mRNA Transcript gene set www.pathwaycomm...
Null mRNA Processing View Gene Set 4.076e-10 158 7.589e-08 6 REACTOME - mRNA Processing gene set www.pathwaycomm...
Null Mitotic M-M/G1 phases View Gene Set 4.844e-09 180 7.729e-07 7 REACTOME - Mitotic M-M/G1 phases gene set www.pathwaycomm...
Null M Phase View Gene Set 8.008e-09 90 1.118e-06 8 REACTOME - M Phase gene set www.pathwaycomm...
Null DNA Replication View Gene Set 2.405e-08 200 2.985e-06 9 REACTOME - DNA Replication gene set www.pathwaycomm...
Null Mitotic Prometaphase View Gene Set 4.771e-08 86 5.329e-06 10 REACTOME - Mitotic Prometaphase gene set www.pathwaycomm...
Null Cell Cycle Mitotic View Gene Set 2.88e-07 312 2.925e-05 11 REACTOME - Cell Cycle Mitotic gene set www.pathwaycomm... Mitotic&format=...
Null Deadenylation of mRNA View Gene Set 4.108e-06 22 0.0003824 12 REACTOME - Deadenylation of mRNA gene set www.pathwaycomm...
Null Metabolism of RNA View Gene Set 5.135e-06 174 0.0004412 13 REACTOME - Metabolism of RNA gene set www.pathwaycomm...
Null Transport of Mature mRNA derived from an Intron-Containing Transcript View Gene Set 8.243e-06 51 0.0006577 14 REACTOME - Transport of Mature mRNA derived from an Intron-Containing Transcript gene set www.pathwaycomm...
Null Post-Elongation Processing of Intron-Containing pre-mRNA View Gene Set 1.266e-05 34 0.0008355 15 REACTOME - Post-Elongation Processing of Intron-Containing pre-mRNA gene set www.pathwaycomm...
Null mRNA 3'-end processing View Gene Set 1.266e-05 34 0.0008355 15 REACTOME - mRNA 3'-end processing gene set www.pathwaycomm...
Null Deadenylation-dependent mRNA decay View Gene Set 1.272e-05 46 0.0008355 15 REACTOME - Deadenylation-dependent mRNA decay gene set www.pathwaycomm...
Null Post-Elongation Processing of the Transcript View Gene Set 1.623e-05 43 0.0009066 18 REACTOME - Post-Elongation Processing of the Transcript gene set www.pathwaycomm...
Null Cleavage of Growing Transcript in the Termination Region View Gene Set 1.623e-05 43 0.0009066 18 REACTOME - Cleavage of Growing Transcript in the Termination Region gene set www.pathwaycomm...
Null RNA Polymerase II Transcription Termination View Gene Set 1.623e-05 43 0.0009066 18 REACTOME - RNA Polymerase II Transcription Termination gene set www.pathwaycomm...
Null Mitotic Telophase /Cytokinesis View Gene Set 2.523e-05 10 0.001342 21 REACTOME - Mitotic Telophase /Cytokinesis gene set www.pathwaycomm...
Null Transport of Mature Transcript to Cytoplasm View Gene Set 3.812e-05 55 0.001935 22 REACTOME - Transport of Mature Transcript to Cytoplasm gene set www.pathwaycomm...
Null Polo-like kinase mediated events View Gene Set 4.573e-05 10 0.002221 23 REACTOME - Polo-like kinase mediated events gene set www.pathwaycomm...
Null Phosphorylation of the APC/C View Gene Set 0.0001821 26 0.008473 24 REACTOME - Phosphorylation of the APC/C gene set www.pathwaycomm...
Null Transcription View Gene Set 0.0002865 178 0.0128 25 REACTOME - Transcription gene set www.pathwaycomm...
Null Interactions of Rev with host cellular proteins View Gene Set 0.000444 33 0.01907 26 REACTOME - Interactions of Rev with host cellular proteins gene set www.pathwaycomm...
Null Metabolism of mRNA View Gene Set 0.0005361 125 0.02113 27 REACTOME - Metabolism of mRNA gene set www.pathwaycomm...
Null snRNP Assembly View Gene Set 0.0005486 50 0.02113 27 REACTOME - snRNP Assembly gene set www.pathwaycomm...
Null Metabolism of non-coding RNA View Gene Set 0.0005486 50 0.02113 27 REACTOME - Metabolism of non-coding RNA gene set www.pathwaycomm...
Null Cell Cycle Checkpoints View Gene Set 0.0006191 124 0.02194 30 REACTOME - Cell Cycle Checkpoints gene set www.pathwaycomm...
Null Pyrimidine biosynthesis View Gene Set 0.0006285 6 0.02194 30 REACTOME - Pyrimidine biosynthesis gene set www.pathwaycomm...
Null Mitotic Metaphase/Anaphase Transition View Gene Set 0.0006117 8 0.02194 30 REACTOME - Mitotic Metaphase/Anaphase Transition gene set www.pathwaycomm...
Null Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins View Gene Set 0.0007805 86 0.02642 33 REACTOME - Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins gene set www.pathwaycomm...
Null Regulation of mitotic cell cycle View Gene Set 0.0008431 95 0.02691 34 REACTOME - Regulation of mitotic cell cycle gene set www.pathwaycomm...
Null APC/C-mediated degradation of cell cycle proteins View Gene Set 0.0008431 95 0.02691 34 REACTOME - APC/C-mediated degradation of cell cycle proteins gene set www.pathwaycomm...
Null Rev-mediated nuclear export of HIV-1 RNA View Gene Set 0.00107 32 0.03144 36 REACTOME - Rev-mediated nuclear export of HIV-1 RNA gene set www.pathwaycomm...
Null Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components View Gene Set 0.001055 18 0.03144 36 REACTOME - Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components gene set www.pathwaycomm...
Null Inactivation of APC/C via direct inhibition of the APC/C complex View Gene Set 0.001055 18 0.03144 36 REACTOME - Inactivation of APC/C via direct inhibition of the APC/C complex gene set www.pathwaycomm...
Null Host Interactions of HIV factors View Gene Set 0.001457 132 0.0397 39 REACTOME - Host Interactions of HIV factors gene set www.pathwaycomm...
Null RNA Polymerase II Transcription View Gene Set 0.001428 101 0.0397 39 REACTOME - RNA Polymerase II Transcription gene set www.pathwaycomm...
Null Regulation of APC/C activators between G1/S and early anaphase View Gene Set 0.001391 88 0.0397 39 REACTOME - Regulation of APC/C activators between G1/S and early anaphase gene set www.pathwaycomm...
Null Nuclear import of Rev protein View Gene Set 0.001526 30 0.04057 42 REACTOME - Nuclear import of Rev protein gene set www.pathwaycomm...
Null Transport of Ribonucleoproteins into the Host Nucleus View Gene Set 0.001602 29 0.04161 43 REACTOME - Transport of Ribonucleoproteins into the Host Nucleus gene set www.pathwaycomm...
Null Phosphorylation of Emi1 View Gene Set 0.001894 12 0.04807 44 REACTOME - Phosphorylation of Emi1 gene set www.pathwaycomm...

Gene Set Collection: tfbsK3Z3

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null V_YY1_02 View Gene Set 7.203e-05 163 0.01534 1 List of genes containing a conserved (FDR < 0.1%) V$YY1_02 TFBS located within 3 kb around the TSS for the YY1 transcription factor www.gene-regula...