Results

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AFA results for: tdrugda2DU

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Gene Set Collection: KEGG

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
KEGG 01100 View Gene Set 1.614e-08 1120 3.454e-06 1 Metabolic pathways www.genome.jp/d...
KEGG 00020 View Gene Set 1.674e-05 31 0.001324 2 Citrate cycle (TCA cycle) www.genome.jp/d...
KEGG 00190 View Gene Set 1.856e-05 134 0.001324 2 Oxidative phosphorylation www.genome.jp/d...
KEGG 04146 View Gene Set 0.0001406 78 0.006208 4 Peroxisome www.genome.jp/d...
KEGG 05012 View Gene Set 0.000145 132 0.006208 4 Parkinson's disease www.genome.jp/d...
KEGG 00280 View Gene Set 0.0007807 44 0.02785 6 Valine leucine and isoleucine degradation www.genome.jp/d...

Gene Set Collection: GO

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
GO GO:0044444 View Gene Set 3.231e-09 5184 4.316e-05 1 cytoplasmic part amigo.geneontol...
GO GO:0031090 View Gene Set 1.33e-08 1905 8.882e-05 2 organelle membrane amigo.geneontol...
GO GO:0045333 View Gene Set 1.908e-07 100 0.0007794 3 cellular respiration amigo.geneontol...
GO GO:0016020 View Gene Set 2.333e-07 7286 0.0007794 3 membrane amigo.geneontol...
GO GO:0005739 View Gene Set 2.95e-07 1274 0.0007883 5 mitochondrion amigo.geneontol...
GO GO:0006091 View Gene Set 4.729e-07 339 0.001053 6 generation of precursor metabolites and energy amigo.geneontol...
GO GO:0044425 View Gene Set 1.07e-06 6145 0.002043 7 membrane part amigo.geneontol...
GO GO:0044431 View Gene Set 1.995e-06 540 0.003332 8 Golgi apparatus part amigo.geneontol...
GO GO:0031224 View Gene Set 4.696e-06 5387 0.006274 9 intrinsic to membrane amigo.geneontol...
GO GO:0044429 View Gene Set 4.299e-06 619 0.006274 9 mitochondrial part amigo.geneontol...
GO GO:0005975 View Gene Set 7.28e-06 550 0.006484 11 carbohydrate metabolic process amigo.geneontol...
GO GO:0015980 View Gene Set 6.555e-06 163 0.006484 11 energy derivation by oxidation of organic compounds amigo.geneontol...
GO GO:0000139 View Gene Set 6.607e-06 450 0.006484 11 Golgi membrane amigo.geneontol...
GO GO:0044455 View Gene Set 7.201e-06 133 0.006484 11 mitochondrial membrane part amigo.geneontol...
GO GO:0016491 View Gene Set 5.785e-06 689 0.006484 11 oxidoreductase activity amigo.geneontol...
GO GO:0016021 View Gene Set 8.117e-06 5278 0.006778 16 integral to membrane amigo.geneontol...
GO GO:0022900 View Gene Set 1.488e-05 115 0.01169 17 electron transport chain amigo.geneontol...
GO GO:0070469 View Gene Set 2.144e-05 77 0.01591 18 respiratory chain amigo.geneontol...
GO GO:0055114 View Gene Set 2.61e-05 647 0.01835 19 oxidation reduction amigo.geneontol...
GO GO:0044262 View Gene Set 2.816e-05 410 0.01881 20 cellular carbohydrate metabolic process amigo.geneontol...
GO GO:0005746 View Gene Set 3.307e-05 70 0.02104 21 mitochondrial respiratory chain amigo.geneontol...
GO GO:0005740 View Gene Set 3.833e-05 444 0.02328 22 mitochondrial envelope amigo.geneontol...
GO GO:0009060 View Gene Set 4.065e-05 34 0.02361 23 aerobic respiration amigo.geneontol...
GO GO:0006120 View Gene Set 5.291e-05 43 0.02541 24 mitochondrial electron transport NADH to ubiquinone amigo.geneontol...
GO GO:0009109 View Gene Set 5.167e-05 27 0.02541 24 coenzyme catabolic process amigo.geneontol...
GO GO:0005737 View Gene Set 5.533e-05 7676 0.02541 24 cytoplasm amigo.geneontol...
GO GO:0031966 View Gene Set 5.706e-05 420 0.02541 24 mitochondrial membrane amigo.geneontol...
GO GO:0003954 View Gene Set 5.583e-05 44 0.02541 24 NADH dehydrogenase activity amigo.geneontol...
GO GO:0008137 View Gene Set 5.583e-05 44 0.02541 24 NADH dehydrogenase (ubiquinone) activity amigo.geneontol...
GO GO:0050136 View Gene Set 5.583e-05 44 0.02541 24 NADH dehydrogenase (quinone) activity amigo.geneontol...
GO GO:0005794 View Gene Set 8.032e-05 893 0.03461 31 Golgi apparatus amigo.geneontol...
GO GO:0006099 View Gene Set 9.714e-05 22 0.038 32 tricarboxylic acid cycle amigo.geneontol...
GO GO:0046356 View Gene Set 9.714e-05 23 0.038 32 acetyl-CoA catabolic process amigo.geneontol...
GO GO:0016651 View Gene Set 9.956e-05 84 0.038 32 oxidoreductase activity acting on NADH or NADPH amigo.geneontol...
GO GO:0048037 View Gene Set 9.408e-05 249 0.038 32 cofactor binding amigo.geneontol...
GO GO:0005743 View Gene Set 0.0001089 305 0.04042 36 mitochondrial inner membrane amigo.geneontol...
GO GO:0050662 View Gene Set 0.0001223 176 0.04416 37 coenzyme binding amigo.geneontol...

Gene Set Collection: Broad.c2.CGP

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad BENPORATH_ES_WITH_H3K27ME3 View Gene Set 4.564e-11 1094 7.775e-08 1 Set 'H3K27 bound': genes posessing the trimethylated H3K27 (H3K27me3) mark in their promoters in human embryonic stem cells as identified by ChIP on chip. www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS_UP View Gene Set 6.501e-11 368 7.775e-08 1 Genes up-regulated by ESRRA [Gene ID=2101] only. www.broad.mit.e...
Broad PEREZ_TP53_TARGETS View Gene Set 1.431e-09 1066 1.141e-06 3 Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of TP53 [Gene ID=7157] off adenoviral vector. www.broad.mit.e...
Broad ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER View Gene Set 2.517e-09 138 1.505e-06 4 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 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN View Gene Set 3.054e-08 485 1.461e-05 5 Genes down-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP View Gene Set 5.628e-08 399 2.244e-05 6 Genes up-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. www.broad.mit.e...
Broad DODD_NASOPHARYNGEAL_CARCINOMA_UP View Gene Set 9.122e-08 1582 2.871e-05 7 Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. www.broad.mit.e...
Broad PEREZ_TP63_TARGETS View Gene Set 9.602e-08 328 2.871e-05 7 Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of the transcriptionally active isoform of TP63 [Gene ID=8626] off adenoviral vector. www.broad.mit.e...
Broad RIGGI_EWING_SARCOMA_PROGENITOR_UP View Gene Set 1.134e-07 399 3.015e-05 9 Genes up-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [Gene ID=2130 2321] fusion protein. www.broad.mit.e...
Broad MOOTHA_HUMAN_MITODB_6_2002 View Gene Set 1.794e-07 420 4.291e-05 10 Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad BENPORATH_SUZ12_TARGETS View Gene Set 2.738e-07 1011 5.954e-05 11 Set 'Suz12 targets': genes identified by ChIP on chip as targets of the Polycomb protein SUZ12 [Gene ID=23512] in human embryonic stem cells. www.broad.mit.e...
Broad BENPORATH_PRC2_TARGETS View Gene Set 4.553e-07 636 9.076e-05 12 Set 'PRC2 targets': Polycomb Repression Complex 2 (PRC) targets; identified by ChIP on chip on human embryonic stem cells as genes that: posess the trimethylated H3K27 mark in their promoters and are bound by SUZ12 [Gene ID=23512] and EED [Gene ID=8726] Polycomb proteins. www.broad.mit.e...
Broad GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP View Gene Set 5.734e-07 180 0.0001055 13 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 ZHAN_MULTIPLE_MYELOMA_PR_UP View Gene Set 7.867e-07 43 0.0001344 14 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 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN View Gene Set 9.977e-07 532 0.0001576 15 Genes differentially expressed in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. www.broad.mit.e...
Broad ALCALAY_AML_BY_NPM1_LOCALIZATION_DN View Gene Set 1.054e-06 179 0.0001576 15 Genes changed in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [Gene ID=4869]: cytoplasmic vs. nucleolar. www.broad.mit.e...
Broad POOLA_INVASIVE_BREAST_CANCER_UP View Gene Set 1.595e-06 278 0.0002244 17 Genes up-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP View Gene Set 1.895e-06 422 0.0002501 18 Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. www.broad.mit.e...
Broad MOOTHA_MITOCHONDRIA View Gene Set 1.986e-06 433 0.0002501 18 Mitochondrial genes www.broad.mit.e...
Broad CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 View Gene Set 3.05e-06 681 0.0003648 20 The 'group 3 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [Gene ID=2099 2064]. www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS View Gene Set 3.441e-06 508 0.0003919 21 Genes regulated by ESRRA [Gene ID=2101] in MCF-7 cells (breast cancer). www.broad.mit.e...
Broad NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP View Gene Set 3.899e-06 87 0.0004239 22 Top 100 probe sets contrubuting to the positive side of the 2nd principal component; associated with adipocytic differentiation. www.broad.mit.e...
Broad RIGGI_EWING_SARCOMA_PROGENITOR_DN View Gene Set 4.819e-06 178 0.0005011 23 Genes down-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [Gene ID=2130 2321] fusion protein. www.broad.mit.e...
Broad CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 View Gene Set 7.359e-06 377 0.0007334 24 The 'group 2 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [Gene ID=2099 2064]. www.broad.mit.e...
Broad LEE_EARLY_T_LYMPHOCYTE_UP View Gene Set 8.872e-06 80 0.0008489 25 Genes up-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. www.broad.mit.e...
Broad BENPORATH_EED_TARGETS View Gene Set 1.335e-05 1033 0.001105 26 Set 'Eed targets': genes identified by ChIP on chip as targets of the Polycomb protein EED [Gene ID=8726] in human embryonic stem cells. www.broad.mit.e...
Broad SMITH_TERT_TARGETS_DN View Gene Set 1.34e-05 71 0.001105 26 Genes consistently down-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [Gene ID=7015] off a retroviral vector. www.broad.mit.e...
Broad CHANG_CYCLING_GENES View Gene Set 1.211e-05 49 0.001105 26 Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. www.broad.mit.e...
Broad HOSHIDA_LIVER_CANCER_SUBCLASS_S3 View Gene Set 1.304e-05 266 0.001105 26 Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. www.broad.mit.e...
Broad CASTELLANO_NRAS_TARGETS_UP View Gene Set 1.664e-05 59 0.001326 30 Genes up-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [Gene ID=4893] knockout mice. www.broad.mit.e...
Broad WALLACE_PROSTATE_CANCER_RACE_UP View Gene Set 2.106e-05 288 0.001603 31 Genes up-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. www.broad.mit.e...
Broad LEE_LIVER_CANCER_SURVIVAL_UP View Gene Set 2.145e-05 130 0.001603 31 Genes highly expressed in hepatocellular carcinoma with good survival. www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_UP View Gene Set 2.507e-05 268 0.001817 33 Genes up-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. www.broad.mit.e...
Broad NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN View Gene Set 2.789e-05 73 0.001962 34 Top 100 probe sets contrubuting to the negative side of the 1st principal component; predominantly associated with synovial sarcoma and myxoid/round cell liposarcoma samples. www.broad.mit.e...
Broad VECCHI_GASTRIC_CANCER_EARLY_DN View Gene Set 3.733e-05 346 0.002551 35 Down-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. www.broad.mit.e...
Broad LINDGREN_BLADDER_CANCER_CLUSTER_3_UP View Gene Set 4.054e-05 314 0.002694 36 Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. www.broad.mit.e...
Broad SMID_BREAST_CANCER_BASAL_DN View Gene Set 5.424e-05 664 0.003506 37 Genes down-regulated in basal subtype of breast cancer samles. www.broad.mit.e...
Broad PEREZ_TP53_AND_TP63_TARGETS View Gene Set 5.88e-05 187 0.003701 38 Genes up-regulated in HMEC cells (primary mammary epithelium) upon expression of both of TP53 [Gene ID=7157] and the transcriptionally active isoform of TP63 [Gene ID=8626] off adenoviral vectors. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP View Gene Set 6.35e-05 135 0.003895 39 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 BROWNE_INTERFERON_RESPONSIVE_GENES View Gene Set 6.609e-05 67 0.003952 40 Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. www.broad.mit.e...
Broad ROZANOV_MMP14_TARGETS_UP View Gene Set 9.314e-05 260 0.005434 41 Genes up-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [Gene ID=4323] compared to those with knockdown of the gene by RNAi. www.broad.mit.e...
Broad BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN View Gene Set 9.833e-05 51 0.0056 42 Down-regulated genes in hepatocellular carcinoma (HCC) subclass G3 defined by unsupervised clustering. www.broad.mit.e...
Broad ONDER_CDH1_TARGETS_2_UP View Gene Set 0.0001057 249 0.005843 43 Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [Gene ID=999] knockdown by RNAi. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN View Gene Set 0.0001075 154 0.005843 43 Top 200 marker genes down-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 LIU_PROSTATE_CANCER_DN View Gene Set 0.0001248 446 0.006534 45 Genes down-regulated in prostate cancer samples. www.broad.mit.e...
Broad HELLER_SILENCED_BY_METHYLATION_UP View Gene Set 0.0001257 247 0.006534 45 Genes up-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. www.broad.mit.e...
Broad CERVERA_SDHB_TARGETS_1_UP View Gene Set 0.0001412 110 0.007185 47 Genes turned on in Hep3B cells (hepatocellular carcinoma HCC) upon knockdown of SDHB [Gene ID=6390] by RNAi. www.broad.mit.e...
Broad NUYTTEN_NIPP1_TARGETS_UP View Gene Set 0.0001845 657 0.009193 48 Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [Gene ID=5511] by RNAi. www.broad.mit.e...
Broad GRABARCZYK_BCL11B_TARGETS_DN View Gene Set 0.0002337 51 0.01141 49 Genes down-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [Gene ID=64919] by RNAi. www.broad.mit.e...
Broad SMID_BREAST_CANCER_LUMINAL_B_UP View Gene Set 0.0003085 162 0.01476 50 Genes up-regulated in the luminal B subtype of breast cancer. www.broad.mit.e...
Broad HUTTMANN_B_CLL_POOR_SURVIVAL_UP View Gene Set 0.000333 268 0.01509 51 Up-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [Gene ID=7535 952] which are associated with poor survival. www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP View Gene Set 0.0003321 153 0.01509 51 Genes up-regulated in CD34+ [Gene ID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [Gene ID=4928 3205] off a retroviral vector at 8 days after transduction. www.broad.mit.e...
Broad CHUNG_BLISTER_CYTOTOXICITY_UP View Gene Set 0.0003345 126 0.01509 51 Genes changed in blister cells from patients with adverse drug reactions (ADR). www.broad.mit.e...
Broad MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN View Gene Set 0.0003501 317 0.01551 54 The postradiation tumor escape signature: genes down-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. www.broad.mit.e...
Broad DOUGLAS_BMI1_TARGETS_UP View Gene Set 0.000363 497 0.01579 55 Genes up-regulated in A4573 cells (Ewing's sarcoma ESFT) after knockdown of BMI1 [Gene ID=648] by RNAi. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN View Gene Set 0.0004033 47 0.01635 56 Genes down-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. www.broad.mit.e...
Broad CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN View Gene Set 0.0003941 163 0.01635 56 Genes down-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402] a protease inhibitor causing apoptosis. www.broad.mit.e...
Broad KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN View Gene Set 0.0003984 56 0.01635 56 Genes down-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. www.broad.mit.e...
Broad SMID_BREAST_CANCER_NORMAL_LIKE_UP View Gene Set 0.0003938 459 0.01635 56 Genes up-regulated in the normal-like subtype of breast cancer. www.broad.mit.e...
Broad BLUM_RESPONSE_TO_SALIRASIB_DN View Gene Set 0.0004345 332 0.01657 60 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 CAIRO_HEPATOBLASTOMA_DN View Gene Set 0.0004357 264 0.01657 60 Genes down-regulated in hepatoblastoma samples compared to normal liver tissue. www.broad.mit.e...
Broad ZHAN_MULTIPLE_MYELOMA_HP_DN View Gene Set 0.0004364 43 0.01657 60 Top 50 down-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. www.broad.mit.e...
Broad MCCLUNG_CREB1_TARGETS_UP View Gene Set 0.0004315 89 0.01657 60 Genes up-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [Gene ID=1385] expression in a transgenic Tet-Off system. www.broad.mit.e...
Broad SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER View Gene Set 0.000453 86 0.01693 64 Genes bearing H3K27me3 mark or whose promoters are bound by the polycomb proteins SUZ12 or EED [Gene ID=23512 8726]; their DNA is methylated de novo in cancer. www.broad.mit.e...
Broad CAIRO_HEPATOBLASTOMA_CLASSES_DN View Gene Set 0.0004614 205 0.01698 65 Genes down-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). www.broad.mit.e...
Broad ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN View Gene Set 0.0004756 258 0.01724 66 Genes down-regulated in macrophages by P.gingivalis FimA pathogen. www.broad.mit.e...
Broad SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP View Gene Set 0.0005118 143 0.018 67 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 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP View Gene Set 0.0005053 61 0.018 67 Up-regulated genes in hepatocellular carcinoma (HCC) subclass G6 defined by unsupervised clustering. www.broad.mit.e...
Broad KOYAMA_SEMA3B_TARGETS_DN View Gene Set 0.0005285 286 0.01832 69 Genes down-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [Gene ID=7869]. www.broad.mit.e...
Broad LIU_VMYB_TARGETS_UP View Gene Set 0.0005503 121 0.01836 70 Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of v-MYB oncogenic varian of CMYB [Gene ID=4602] off adenovirus vector. www.broad.mit.e...
Broad GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN View Gene Set 0.0005525 86 0.01836 70 Genes down-regulated in quiescent vs dividing CD34+ [Gene ID=8842] cells isolated from peripheral blood of normal donors. www.broad.mit.e...
Broad WONG_MITOCHONDRIA_GENE_MODULE View Gene Set 0.0005432 208 0.01836 70 Genes that comprise the mitochondria gene module www.broad.mit.e...
Broad LEE_TARGETS_OF_PTCH1_AND_SUFU_UP View Gene Set 0.0005783 77 0.01839 73 Genes up-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [Gene ID=5727 51684] in conjunction with TP53 [Gene ID=7157] loss. www.broad.mit.e...
Broad CROONQUIST_IL6_DEPRIVATION_DN View Gene Set 0.0005843 80 0.01839 73 Genes down-regulated in the ANBL-6 cell line (multiple myeloma MM) after withdrawal of IL6 [Gene ID=3569]. www.broad.mit.e...
Broad BAELDE_DIABETIC_NEPHROPATHY_DN View Gene Set 0.0005697 35 0.01839 73 Top 50 down-regulated genes in glomeruli from kidneys with diabetic nephropathy (type 2 diabetes mellitus). www.broad.mit.e...
Broad MOOTHA_TCA View Gene Set 0.000579 15 0.01839 73 Tricarboxylic acid related genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad HORIUCHI_WTAP_TARGETS_UP View Gene Set 0.0006192 284 0.01924 77 Genes up-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [Gene ID=9589] by RNAi. www.broad.mit.e...
Broad KAAB_HEART_ATRIUM_VS_VENTRICLE_DN View Gene Set 0.0006688 257 0.02051 78 Genes up-regulated in the ventricles of healthy hearts compared to atria. www.broad.mit.e...
Broad GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP View Gene Set 0.0007123 131 0.02155 79 Up-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [Gene ID=4299 4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. www.broad.mit.e...
Broad BERENJENO_TRANSFORMED_BY_RHOA_DN View Gene Set 0.0007209 353 0.02155 79 Genes down-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 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN View Gene Set 0.0007691 296 0.02271 81 Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. www.broad.mit.e...
Broad LINDGREN_BLADDER_CANCER_CLUSTER_1_DN View Gene Set 0.0008134 368 0.02344 82 Genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. www.broad.mit.e...
Broad MOOTHA_VOXPHOS View Gene Set 0.0008061 82 0.02344 82 Genes involved in oxidative phosphorylation; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP View Gene Set 0.0008419 38 0.02397 84 Genes up-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. www.broad.mit.e...
Broad SANA_RESPONSE_TO_IFNG_UP View Gene Set 0.0008787 68 0.02473 85 Genes up-regulated in five primary endothelial cell types (lung aortic iliac dermal and colon) by IFNG [Gene ID=3458]. www.broad.mit.e...
Broad WIELAND_UP_BY_HBV_INFECTION View Gene Set 0.0009665 98 0.02688 86 Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. www.broad.mit.e...
Broad ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP View Gene Set 0.001149 178 0.03055 87 Genes up-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 LANDIS_ERBB2_BREAST_TUMORS_324_DN View Gene Set 0.001132 137 0.03055 87 The 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [Gene ID=2064]. www.broad.mit.e...
Broad MANALO_HYPOXIA_UP View Gene Set 0.001133 197 0.03055 87 Genes up-regulated in response to both hypoxia and overexpression of an active form of HIF1A [Gene ID=3091]. www.broad.mit.e...
Broad ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP View Gene Set 0.00115 24 0.03055 87 Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and up-regulated by further treatment with ribavirin [PubChem=5064]. www.broad.mit.e...
Broad DELYS_THYROID_CANCER_DN View Gene Set 0.001181 213 0.03104 91 Genes down-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. www.broad.mit.e...
Broad LINDGREN_BLADDER_CANCER_CLUSTER_2B View Gene Set 0.001267 384 0.03294 92 Genes specifically up-regulated in Cluster IIb of urothelial cell carcinom (UCC) tumors. www.broad.mit.e...
Broad SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP View Gene Set 0.00131 72 0.0337 93 Genes up-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). www.broad.mit.e...
Broad BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN View Gene Set 0.001335 51 0.03397 94 Down-regulated genes in hepatocellular carcinoma (HCC) subclass G123 defined by unsupervised clustering. www.broad.mit.e...
Broad LIU_CMYB_TARGETS_UP View Gene Set 0.001485 158 0.03662 95 Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [Gene ID=4602] off adenovirus vector. www.broad.mit.e...
Broad MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN View Gene Set 0.001476 53 0.03662 95 Genes commonly down-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [Gene ID=595 1019]. www.broad.mit.e...
Broad GOLDRATH_ANTIGEN_RESPONSE View Gene Set 0.001465 315 0.03662 95 Genes up-regulated at the peak of an antigen response of naive CD8+ [Gene ID=925 926] T-cells. www.broad.mit.e...
Broad KANG_DOXORUBICIN_RESISTANCE_UP View Gene Set 0.00165 53 0.04003 98 Genes differentialy expressed in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. www.broad.mit.e...
Broad BROWNE_HCMV_INFECTION_48HR_UP View Gene Set 0.001657 175 0.04003 98 Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not up-regulated at the previous time point 24 h. www.broad.mit.e...
Broad GAL_LEUKEMIC_STEM_CELL_DN View Gene Set 0.001793 239 0.04246 100 Genes down-regulated in leukemic stem cells (LSC) defined as CD34+CD38- [Gene ID=947 952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. www.broad.mit.e...
Broad RICKMAN_HEAD_AND_NECK_CANCER_A View Gene Set 0.001777 91 0.04246 100 Cluster a: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). www.broad.mit.e...
Broad DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP View Gene Set 0.00186 317 0.04278 102 Genes up-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. www.broad.mit.e...
Broad GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP View Gene Set 0.001843 86 0.04278 102 Genes up-regulated in quiescent (G0) CD34+ [Gene ID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. www.broad.mit.e...
Broad CHENG_IMPRINTED_BY_ESTRADIOL View Gene Set 0.001845 104 0.04278 102 Genes whose CpG islands became hypermethylated in breast progenitor cells pre-exposed to estradiol [PubChem=5757]. www.broad.mit.e...
Broad CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY View Gene Set 0.00193 27 0.04396 105 Genes down-regulated in T cell acute lymphocytic leukemia (T-ALL) patients refractory to chemotherapy treatment. www.broad.mit.e...
Broad TRAYNOR_RETT_SYNDROM_UP View Gene Set 0.001983 22 0.04476 106 Genes up-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [Gene ID=4204]. www.broad.mit.e...
Broad GOLDRATH_IMMUNE_MEMORY View Gene Set 0.002058 57 0.04601 107 'Memory genes' expressed uniquely in CD8+ [Gene ID=925] memory T lymphocytes (compared with effector or na??ve cells) www.broad.mit.e...
Broad JI_METASTASIS_REPRESSED_BY_STK11 View Gene Set 0.00222 23 0.04917 108 Adenocarcinoma metastatic program genes up-regulated in A549 and H2126 cells (lung cancer) lacking functional STK11 [Gene ID=6794] but down-regulated by the normal gene. www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.KEGG

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad KEGG_CITRATE_CYCLE_TCA_CYCLE View Gene Set 1.674e-05 32 0.001726 1 Citrate cycle (TCA cycle) www.broad.mit.e...
Broad KEGG_OXIDATIVE_PHOSPHORYLATION View Gene Set 1.856e-05 135 0.001726 1 Oxidative phosphorylation www.broad.mit.e...
Broad KEGG_PEROXISOME View Gene Set 0.0001406 78 0.006745 3 Peroxisome www.broad.mit.e...
Broad KEGG_PARKINSONS_DISEASE View Gene Set 0.000145 133 0.006745 3 Parkinson's disease www.broad.mit.e...
Broad KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION View Gene Set 0.0007807 44 0.02904 5 Valine leucine and isoleucine degradation www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.REACTOME

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad REACTOME_ELECTRON_TRANSPORT_CHAIN View Gene Set 2.012e-06 75 0.0008653 1 Genes involved in Electron Transport Chain www.broad.mit.e...
Broad REACTOME_GLUCOSE_REGULATION_OF_INSULIN_SECRETION View Gene Set 2.188e-05 161 0.004705 2 Genes involved in Glucose Regulation of Insulin Secretion www.broad.mit.e...
Broad REACTOME_REGULATION_OF_INSULIN_SECRETION View Gene Set 6.332e-05 212 0.009076 3 Genes involved in Regulation of Insulin Secretion www.broad.mit.e...
Broad REACTOME_CITRIC_ACID_CYCLE View Gene Set 9.026e-05 19 0.009703 4 Genes involved in Citric acid cycle (TCA cycle) www.broad.mit.e...
Broad REACTOME_APCDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B View Gene Set 0.0003141 18 0.02701 5 Genes involved in APC/C:Cdc20 mediated degradation of Cyclin B www.broad.mit.e...

Gene Set Collection: Broad.c4.CGN

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad GNF2_CCNB2 View Gene Set 5.665e-05 53 0.02419 1 Neighborhood of CCNB2 www.broad.mit.e...

Gene Set Collection: Broad.c4.CM

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad module_66 View Gene Set 6.865e-11 530 1.558e-08 1 Genes in module_66 www.broad.mit.e...
Broad module_100 View Gene Set 4.597e-11 523 1.558e-08 1 Genes in module_100 www.broad.mit.e...
Broad module_137 View Gene Set 2.092e-10 525 3.166e-08 3 Genes in module_137 www.broad.mit.e...
Broad module_11 View Gene Set 9.566e-09 520 1.086e-06 4 Genes in module_11 www.broad.mit.e...
Broad module_491 View Gene Set 2.74e-06 74 0.0002488 5 Genes in module_491 www.broad.mit.e...
Broad module_568 View Gene Set 7.667e-06 70 0.0005801 6 Genes in module_568 www.broad.mit.e...
Broad module_129 View Gene Set 1.316e-05 215 0.000747 7 Genes in module_129 www.broad.mit.e...
Broad module_171 View Gene Set 1.21e-05 131 0.000747 7 Genes in module_171 www.broad.mit.e...
Broad module_93 View Gene Set 1.802e-05 180 0.0009092 9 Genes in module_93 www.broad.mit.e...
Broad module_345 View Gene Set 3.343e-05 118 0.001518 10 Genes in module_345 www.broad.mit.e...
Broad module_305 View Gene Set 3.909e-05 19 0.001613 11 Genes in module_305 www.broad.mit.e...
Broad module_40 View Gene Set 6.887e-05 81 0.001983 12 Genes in module_40 www.broad.mit.e...
Broad module_43 View Gene Set 6.178e-05 97 0.001983 12 Genes in module_43 www.broad.mit.e...
Broad module_84 View Gene Set 7.424e-05 526 0.001983 12 Genes in module_84 www.broad.mit.e...
Broad module_119 View Gene Set 6.73e-05 135 0.001983 12 Genes in module_119 www.broad.mit.e...
Broad module_212 View Gene Set 7.018e-05 316 0.001983 12 Genes in module_212 www.broad.mit.e...
Broad module_436 View Gene Set 7.235e-05 129 0.001983 12 Genes in module_436 www.broad.mit.e...
Broad module_208 View Gene Set 0.000101 118 0.002547 18 Genes in module_208 www.broad.mit.e...
Broad module_152 View Gene Set 0.0001618 121 0.003866 19 Genes in module_152 www.broad.mit.e...
Broad module_62 View Gene Set 0.0001818 88 0.003974 20 Genes in module_62 www.broad.mit.e...
Broad module_88 View Gene Set 0.0001838 812 0.003974 20 Genes in module_88 www.broad.mit.e...
Broad module_55 View Gene Set 0.0003286 807 0.006781 22 Genes in module_55 www.broad.mit.e...
Broad module_77 View Gene Set 0.0005014 28 0.009898 23 Genes in module_77 www.broad.mit.e...
Broad module_19 View Gene Set 0.0006536 306 0.01231 24 Genes in module_19 www.broad.mit.e...
Broad module_23 View Gene Set 0.0006777 552 0.01231 24 Genes in module_23 www.broad.mit.e...
Broad module_221 View Gene Set 0.0007455 30 0.01302 26 Genes in module_221 www.broad.mit.e...
Broad module_184 View Gene Set 0.0007932 29 0.01334 27 Genes in module_184 www.broad.mit.e...
Broad module_293 View Gene Set 0.0008859 12 0.01436 28 Genes in module_293 www.broad.mit.e...
Broad module_143 View Gene Set 0.0009292 14 0.01455 29 Genes in module_143 www.broad.mit.e...
Broad module_292 View Gene Set 0.001181 129 0.0173 30 Genes in module_292 www.broad.mit.e...
Broad module_307 View Gene Set 0.001152 24 0.0173 30 Genes in module_307 www.broad.mit.e...
Broad module_12 View Gene Set 0.001734 346 0.02461 32 Genes in module_12 www.broad.mit.e...
Broad module_426 View Gene Set 0.001831 82 0.02519 33 Genes in module_426 www.broad.mit.e...
Broad module_205 View Gene Set 0.002159 259 0.02882 34 Genes in module_205 www.broad.mit.e...
Broad module_144 View Gene Set 0.003284 8 0.0426 35 Genes in module_144 www.broad.mit.e...
Broad module_42 View Gene Set 0.003937 25 0.04965 36 Genes in module_42 www.broad.mit.e...

Gene Set Collection: Broad.c5.BP

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad CARBOHYDRATE_METABOLIC_PROCESS View Gene Set 5.826e-05 175 0.04807 1 Genes annotated by the GO term GO:0005975. The chemical reactions and pathways involving carbohydrates any of a group of organic compounds based of the general formula Cx(H2O)y. www.broad.mit.e...

Gene Set Collection: Broad.c5.CC

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Broad MICROBODY View Gene Set 0.0003811 46 0.0444 1 Genes annotated by the GO term GO:0042579. Cytoplasmic organelles spherical or oval in shape that are bounded by a single membrane and contain oxidative enzymes especially those utilizing hydrogen peroxide (H2O2). www.broad.mit.e...
Broad PEROXISOME View Gene Set 0.0003811 46 0.0444 1 Genes annotated by the GO term GO:0005777. A small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2). www.broad.mit.e...

Gene Set Collection: PMID

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
PMID 12975309 View Gene Set 1.549e-05 1000 0.03884 1 The secreted protein discovery initiative (SPDI) a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. www.ncbi.nlm.ni...

Gene Set Collection: pathwayCommons.humancyc

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null TCA cycle View Gene Set 7.12e-05 13 0.01851 1 HUMANCYC - TCA cycle gene set www.pathwaycomm...

Gene Set Collection: pathwayCommons.reactome

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null Respiratory electron transport View Gene Set 2.012e-06 76 0.002248 1 REACTOME - Respiratory electron transport gene set www.pathwaycomm...
Null Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins. View Gene Set 7.531e-06 91 0.004206 2 REACTOME - Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins. gene set www.pathwaycomm... ATP synthesis b... and heat produc...
Null Post-chaperonin tubulin folding pathway View Gene Set 5.618e-05 13 0.02092 3 REACTOME - Post-chaperonin tubulin folding pathway gene set www.pathwaycomm...
Null Citric acid cycle (TCA cycle) View Gene Set 9.026e-05 19 0.02521 4 REACTOME - Citric acid cycle (TCA cycle) gene set www.pathwaycomm...
Null APC/C:Cdc20 mediated degradation of Cyclin B View Gene Set 0.0002129 22 0.04755 5 REACTOME - APC/C:Cdc20 mediated degradation of Cyclin B gene set www.pathwaycomm...

Gene Set Collection: mirbase.targets

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

Gene Set Name GeneSetDescription Value Gene Set Size Corrected Value Ranking Description URL
Null hsa-miR-206 View Gene Set 9.713e-06 683 0.006906 1 microRNA targets for hsa-miR-206 from mirbase.targets www.mirbase.org...
Null hsa-miR-146a View Gene Set 4.986e-05 717 0.01773 2 microRNA targets for hsa-miR-146a from mirbase.targets www.mirbase.org...
Null hsa-miR-124* View Gene Set 0.0001179 599 0.02793 3 microRNA targets for hsa-miR-124* from mirbase.targets www.mirbase.org...