Results

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Go to: Gene Set Collection: GO
Go to: Gene Set Collection: Broad.c1.CYTOBAND
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Go to: Gene Set Collection: Broad.c2.CP.REACTOME
Go to: Gene Set Collection: Broad.c4.CM
Go to: Gene Set Collection: PMID
Go to: Gene Set Collection: ChromosomalTiles5Mb
Go to: Gene Set Collection: Prosite
Go to: Gene Set Collection: pathwayCommons.reactome
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Go to: Gene Set Collection: hprdBatch.DIFFERENT

AFA results for: tlineda4SAHA

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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:0005739 View Gene Set 3.101e-07 1274 0.004143 1 mitochondrion amigo.geneontol...

Gene Set Collection: Broad.c1.CYTOBAND

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 chr8q24 View Gene Set 7.975e-23 162 2.6e-20 1 Genes in cytogenetic band chr8q24 www.broad.mit.e...
Broad chr19p13 View Gene Set 6.148e-16 514 1.002e-13 2 Genes in cytogenetic band chr19p13 www.broad.mit.e...
Broad chr3p25 View Gene Set 1.13e-09 83 1.228e-07 3 Genes in cytogenetic band chr3p25 www.broad.mit.e...
Broad chr8q22 View Gene Set 5.33e-08 80 4.344e-06 4 Genes in cytogenetic band chr8q22 www.broad.mit.e...
Broad chr2q12 View Gene Set 1.556e-07 48 1.015e-05 5 Genes in cytogenetic band chr2q12 www.broad.mit.e...
Broad chr3p21 View Gene Set 2.552e-07 226 1.387e-05 6 Genes in cytogenetic band chr3p21 www.broad.mit.e...
Broad chr20q11 View Gene Set 1.02e-06 119 4.752e-05 7 Genes in cytogenetic band chr20q11 www.broad.mit.e...
Broad chrxp11 View Gene Set 1.315e-06 224 5.358e-05 8 Genes in cytogenetic band chrxp11 www.broad.mit.e...
Broad chr3q13 View Gene Set 3.504e-06 96 0.0001269 9 Genes in cytogenetic band chr3q13 www.broad.mit.e...
Broad chr14q23 View Gene Set 4.059e-06 62 0.0001323 10 Genes in cytogenetic band chr14q23 www.broad.mit.e...
Broad chr3q12 View Gene Set 7.604e-06 42 0.0002254 11 Genes in cytogenetic band chr3q12 www.broad.mit.e...
Broad chr8q21 View Gene Set 9.053e-06 73 0.0002459 12 Genes in cytogenetic band chr8q21 www.broad.mit.e...
Broad chr20q13 View Gene Set 2.872e-05 183 0.0007202 13 Genes in cytogenetic band chr20q13 www.broad.mit.e...
Broad chr3p22 View Gene Set 3.357e-05 64 0.0007296 14 Genes in cytogenetic band chr3p22 www.broad.mit.e...
Broad chr17q25 View Gene Set 3.317e-05 172 0.0007296 14 Genes in cytogenetic band chr17q25 www.broad.mit.e...
Broad chr20p12 View Gene Set 4.798e-05 45 0.0009776 16 Genes in cytogenetic band chr20p12 www.broad.mit.e...
Broad chrxp22 View Gene Set 5.496e-05 158 0.001054 17 Genes in cytogenetic band chrxp22 www.broad.mit.e...
Broad chrxq22 View Gene Set 6.849e-05 102 0.00124 18 Genes in cytogenetic band chrxq22 www.broad.mit.e...
Broad chr1q41 View Gene Set 8.945e-05 41 0.001535 19 Genes in cytogenetic band chr1q41 www.broad.mit.e...
Broad chr2p11 View Gene Set 9.878e-05 143 0.001537 20 Genes in cytogenetic band chr2p11 www.broad.mit.e...
Broad chr11q13 View Gene Set 9.898e-05 276 0.001537 20 Genes in cytogenetic band chr11q13 www.broad.mit.e...
Broad chr20p11 View Gene Set 0.0001126 73 0.001593 22 Genes in cytogenetic band chr20p11 www.broad.mit.e...
Broad chrxq26 View Gene Set 0.0001154 70 0.001593 22 Genes in cytogenetic band chrxq26 www.broad.mit.e...
Broad chrxq24 View Gene Set 0.0001173 44 0.001593 22 Genes in cytogenetic band chrxq24 www.broad.mit.e...
Broad chr11q24 View Gene Set 0.000289 95 0.003768 25 Genes in cytogenetic band chr11q24 www.broad.mit.e...
Broad chrxq28 View Gene Set 0.0003105 145 0.003894 26 Genes in cytogenetic band chrxq28 www.broad.mit.e...
Broad chr3p24 View Gene Set 0.0003383 47 0.004085 27 Genes in cytogenetic band chr3p24 www.broad.mit.e...
Broad chrxq13 View Gene Set 0.0004281 75 0.004984 28 Genes in cytogenetic band chrxq13 www.broad.mit.e...
Broad chr11q23 View Gene Set 0.0005379 124 0.006047 29 Genes in cytogenetic band chr11q23 www.broad.mit.e...
Broad chr17q23 View Gene Set 0.0006056 77 0.006581 30 Genes in cytogenetic band chr17q23 www.broad.mit.e...
Broad chr4q12 View Gene Set 0.0008066 44 0.008482 31 Genes in cytogenetic band chr4q12 www.broad.mit.e...
Broad chr10q22 View Gene Set 0.0008601 109 0.008762 32 Genes in cytogenetic band chr10q22 www.broad.mit.e...
Broad chr19q13 View Gene Set 0.001168 765 0.01154 33 Genes in cytogenetic band chr19q13 www.broad.mit.e...
Broad chr11p11 View Gene Set 0.001332 100 0.01277 34 Genes in cytogenetic band chr11p11 www.broad.mit.e...
Broad chr2q13 View Gene Set 0.002185 39 0.02035 35 Genes in cytogenetic band chr2q13 www.broad.mit.e...
Broad chr3q11 View Gene Set 0.002688 20 0.02434 36 Genes in cytogenetic band chr3q11 www.broad.mit.e...
Broad chr1p36 View Gene Set 0.002781 385 0.02451 37 Genes in cytogenetic band chr1p36 www.broad.mit.e...
Broad chr20p13 View Gene Set 0.003326 76 0.02854 38 Genes in cytogenetic band chr20p13 www.broad.mit.e...
Broad chr2q11 View Gene Set 0.003532 69 0.02953 39 Genes in cytogenetic band chr2q11 www.broad.mit.e...
Broad chr11q12 View Gene Set 0.004767 179 0.03885 40 Genes in cytogenetic band chr11q12 www.broad.mit.e...
Broad chr4q13 View Gene Set 0.005235 74 0.04162 41 Genes in cytogenetic band chr4q13 www.broad.mit.e...
Broad chr2q View Gene Set 0.005715 9 0.04436 42 Genes in cytogenetic band chr2q www.broad.mit.e...
Broad chr2q37 View Gene Set 0.006017 143 0.04562 43 Genes in cytogenetic band chr2q37 www.broad.mit.e...
Broad chr10q21 View Gene Set 0.00621 52 0.04601 44 Genes in cytogenetic band chr10q21 www.broad.mit.e...

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 NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON View Gene Set 2.866e-26 150 6.855e-23 1 Genes within amplicon 8q23-q24 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad COLDREN_GEFITINIB_RESISTANCE_DN View Gene Set 2.829e-18 217 3.384e-15 2 Genes down-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 NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON View Gene Set 1.845e-13 128 1.471e-10 3 Genes within amplicon 8q12-q22 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN View Gene Set 8.245e-11 920 4.931e-08 4 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 ONDER_CDH1_TARGETS_2_DN View Gene Set 8.513e-10 453 4.073e-07 5 Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [Gene ID=999] knockdown by RNAi. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP View Gene Set 1.496e-09 422 5.964e-07 6 Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP View Gene Set 2.566e-09 114 7.671e-07 7 Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. www.broad.mit.e...
Broad VECCHI_GASTRIC_CANCER_EARLY_UP View Gene Set 2.528e-09 408 7.671e-07 7 Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN View Gene Set 3.46e-09 832 9.195e-07 9 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 WEI_MYCN_TARGETS_WITH_E_BOX View Gene Set 3.894e-09 757 9.315e-07 10 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 CAIRO_HEPATOBLASTOMA_CLASSES_UP View Gene Set 1.887e-08 577 4.103e-06 11 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 MOOTHA_MITOCHONDRIA View Gene Set 2.634e-08 433 5.251e-06 12 Mitochondrial genes www.broad.mit.e...
Broad DAIRKEE_TERT_TARGETS_UP View Gene Set 2.096e-07 317 3.857e-05 13 Genes up-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [Gene ID=7015] off a retroviral vector. www.broad.mit.e...
Broad GRADE_COLON_CANCER_UP View Gene Set 2.614e-07 711 4.466e-05 14 Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. www.broad.mit.e...
Broad NUYTTEN_EZH2_TARGETS_DN View Gene Set 8.698e-07 859 0.0001387 15 Genes down-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [Gene ID=2146] by RNAi. www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_DN View Gene Set 1.039e-06 136 0.0001553 16 Genes down-regulated in MCF7 cells (breast cancer) under hypoxia conditions. www.broad.mit.e...
Broad KANG_DOXORUBICIN_RESISTANCE_UP View Gene Set 1.191e-06 53 0.0001676 17 Genes differentialy expressed in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. www.broad.mit.e...
Broad MOOTHA_HUMAN_MITODB_6_2002 View Gene Set 3.18e-06 420 0.0004226 18 Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad LY_AGING_MIDDLE_DN View Gene Set 3.426e-06 15 0.0004313 19 Genes down-regulated in fibroblasts from middle-age individuals compared to those from the young donors. www.broad.mit.e...
Broad TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C View Gene Set 4.514e-06 436 0.0005399 20 Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [Gene ID=407041 407042] microRNAs. www.broad.mit.e...
Broad NUYTTEN_NIPP1_TARGETS_DN View Gene Set 4.958e-06 758 0.0005604 21 Genes down-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [Gene ID=5511] by RNAi. www.broad.mit.e...
Broad KOBAYASHI_EGFR_SIGNALING_24HR_DN View Gene Set 5.154e-06 243 0.0005604 21 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 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP View Gene Set 5.604e-06 143 0.0005828 23 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 LY_AGING_OLD_DN View Gene Set 9.371e-06 47 0.000934 24 Genes up-regulated in fibroblasts from old individuals compared to those from young donors. www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN View Gene Set 1.725e-05 46 0.00165 25 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 NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON View Gene Set 1.901e-05 317 0.001749 26 Genes within amplicon 17q21-q25 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad MANALO_HYPOXIA_DN View Gene Set 2.274e-05 276 0.002015 27 Genes down-regulated in response to both hypoxia and overexpression of an active form of HIF1A [Gene ID=3091]. www.broad.mit.e...
Broad OKAWA_NEUROBLASTOMA_1P36_31_DELETION View Gene Set 2.414e-05 23 0.002062 28 Genes in the smallest region of deletion (SRD) in 1p36.3 area in neuroblastoma samples. www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON View Gene Set 2.902e-05 134 0.002362 29 Genes within amplicon 20q12-q13 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 View Gene Set 2.962e-05 435 0.002362 29 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 AMIT_EGF_RESPONSE_120_MCF10A View Gene Set 4.724e-05 41 0.003645 31 Genes whose expression peaked at 120 min after stimulation of MCF10A cells with EGF [Gene ID=1950]. www.broad.mit.e...
Broad CROONQUIST_IL6_DEPRIVATION_DN View Gene Set 5.089e-05 80 0.003804 32 Genes down-regulated in the ANBL-6 cell line (multiple myeloma MM) after withdrawal of IL6 [Gene ID=3569]. www.broad.mit.e...
Broad LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT View Gene Set 7.536e-05 100 0.005463 33 Genes downregulated in MCF10A cells (breast cancer) co-cultured with cancer-associated fibroblasts (CAF). www.broad.mit.e...
Broad BERENJENO_TRANSFORMED_BY_RHOA_UP View Gene Set 0.0001049 485 0.007379 34 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 LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED View Gene Set 0.0001285 16 0.008781 35 X chromosome and imprinted genes up-regulated in HeLa cells (cervical cancer) after knockdown of the MBD (methyl-CpG binding domain) proteins by RNAi. www.broad.mit.e...
Broad LIU_PROSTATE_CANCER_UP View Gene Set 0.0001667 88 0.01013 36 Genes up-regulated in prostate cancer samples. www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON View Gene Set 0.0001539 8 0.01013 36 Genes within amplicon 10q22 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad ONDER_CDH1_TARGETS_3_DN View Gene Set 0.0001598 52 0.01013 36 Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [Gene ID=999] which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS_UP View Gene Set 0.0001693 368 0.01013 36 Genes up-regulated by ESRRA [Gene ID=2101] only. www.broad.mit.e...
Broad AMUNDSON_GAMMA_RADIATION_RESPONSE View Gene Set 0.0001623 36 0.01013 36 Genes down-regulated across the entire panel of NCI-60 cell lines in response to gamma radiation. www.broad.mit.e...
Broad ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER View Gene Set 0.000198 138 0.01155 41 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 SCHUHMACHER_MYC_TARGETS_UP View Gene Set 0.0002096 68 0.01194 42 Genes up-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [Gene ID=4609]. www.broad.mit.e...
Broad ONDER_CDH1_TARGETS_1_DN View Gene Set 0.0002502 161 0.01392 43 Genes down-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [Gene ID=999]. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP View Gene Set 0.0002801 135 0.01522 44 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 ELVIDGE_HIF1A_TARGETS_UP View Gene Set 0.0003097 64 0.01529 45 Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [Gene ID=3091] by RNAi. www.broad.mit.e...
Broad OLSSON_E2F3_TARGETS_DN View Gene Set 0.000302 28 0.01529 45 Genes down-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [Gene ID=1871] by RNAi. www.broad.mit.e...
Broad LE_EGR2_TARGETS_UP View Gene Set 0.0002919 100 0.01529 45 Genes up-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [Gene ID=1959]. www.broad.mit.e...
Broad HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP View Gene Set 0.0003081 93 0.01529 45 Genes up-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. www.broad.mit.e...
Broad WINNEPENNINCKX_MELANOMA_METASTASIS_UP View Gene Set 0.0003144 152 0.01529 45 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 SESTO_RESPONSE_TO_UV_C3 View Gene Set 0.0003197 20 0.01529 45 Cluster 3: genes changed in primary keratinocytes by UVB irradiation. www.broad.mit.e...
Broad CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN View Gene Set 0.0003429 163 0.0159 51 Genes down-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402] a protease inhibitor causing apoptosis. www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON View Gene Set 0.0003457 150 0.0159 51 Genes within amplicon 11q12-q14 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad WONG_MITOCHONDRIA_GENE_MODULE View Gene Set 0.0003644 208 0.01614 53 Genes that comprise the mitochondria gene module www.broad.mit.e...
Broad CROONQUIST_NRAS_SIGNALING_DN View Gene Set 0.0003592 62 0.01614 53 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 DODD_NASOPHARYNGEAL_CARCINOMA_DN View Gene Set 0.0004162 1253 0.0181 55 Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. www.broad.mit.e...
Broad WONG_EMBRYONIC_STEM_CELL_CORE View Gene Set 0.0004407 331 0.01883 56 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 BIERIE_INFLAMMATORY_RESPONSE_TGFB1 View Gene Set 0.0004879 5 0.02048 57 Inflammatory genes down-regulated in mammary carcinoma cells after stimulation with TGFB1 [Gene ID=7040] for 1 hr. www.broad.mit.e...
Broad GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP View Gene Set 0.0005103 180 0.0208 58 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 MOOTHA_TCA View Gene Set 0.0005129 15 0.0208 58 Tricarboxylic acid related genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN View Gene Set 0.0005684 86 0.02266 60 Genes down-regulated in quiescent vs dividing CD34+ [Gene ID=8842] cells isolated from peripheral blood of normal donors. www.broad.mit.e...
Broad TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP View Gene Set 0.0006299 19 0.0247 61 Genes up-regulated in ductal vs lobular carcinoma breast tumor cells. www.broad.mit.e...
Broad LINDGREN_BLADDER_CANCER_CLUSTER_3_UP View Gene Set 0.0006935 314 0.02633 62 Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. www.broad.mit.e...
Broad LY_AGING_PREMATURE_DN View Gene Set 0.0006893 24 0.02633 62 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 HEDENFALK_BREAST_CANCER_BRACX_UP View Gene Set 0.0007321 17 0.02736 64 Up-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [Gene ID=672 675] breast tumors (BRACx): group A vs group B. www.broad.mit.e...
Broad CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP View Gene Set 0.000812 34 0.02988 65 Genes in the AKT1 [Gene ID=207] pathway which are independent of MTOR [Gene ID=2475] insensitive to RAD001 (everolimus) [PubChem=6442177]. www.broad.mit.e...
Broad AIGNER_ZEB1_TARGETS View Gene Set 0.0008569 29 0.03106 66 Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [Gene ID=6935] by RNAi. www.broad.mit.e...
Broad MOOTHA_PYR View Gene Set 0.0009602 8 0.03378 67 Genes involved in pyruvate metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad MOOTHA_ROS View Gene Set 0.0009602 8 0.03378 67 Reactive oxidative species (ROS) genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad MCBRYAN_PUBERTAL_BREAST_4_5WK_UP View Gene Set 0.001091 243 0.03782 69 Genes up-regulated during pubertal mammary gland development between week 4 and 5. www.broad.mit.e...
Broad SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP View Gene Set 0.001176 72 0.04019 70 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 NIKOLSKY_BREAST_CANCER_19Q13.4_AMPLICON View Gene Set 0.001323 7 0.04438 71 Genes within amplicon 19q13.4 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP View Gene Set 0.001336 116 0.04438 71 Up-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2)[PubChem=1573]. www.broad.mit.e...
Broad DANG_MYC_TARGETS_UP View Gene Set 0.001374 127 0.04501 73 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 BILD_MYC_ONCOGENIC_SIGNATURE View Gene Set 0.00147 187 0.04688 74 Genes selected in supervised analyses to discriminate cells expressing c-Myc [Gene ID=4609] from control cells expressing GFP. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN View Gene Set 0.001467 144 0.04688 74 Top 200 marker genes down-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [Gene ID=1499]. www.broad.mit.e...
Broad CHANG_CYCLING_GENES View Gene Set 0.001533 49 0.04825 76 Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. www.broad.mit.e...
Broad WALLACE_PROSTATE_CANCER_UP View Gene Set 0.001591 18 0.04882 77 Genes up-regulated in prostate tumor vs normal tissue samples. www.broad.mit.e...
Broad RUIZ_TNC_TARGETS_DN View Gene Set 0.001592 138 0.04882 77 Genes down-regulated in T98G cells (glioblastoma) by TNC [Gene ID=3371]. 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_RNA_POLYMERASE_I_CHAIN_ELONGATION View Gene Set 1.515e-06 34 0.0006513 1 Genes involved in RNA PolymeraseChain Elongation www.broad.mit.e...
Broad REACTOME_PYRUVATE_METABOLISM_AND_TCA_CYCLE View Gene Set 3.261e-05 36 0.007011 2 Genes involved in Pyruvate metabolism and TCA cycle www.broad.mit.e...
Broad REACTOME_MITOTIC_PROMETAPHASE View Gene Set 0.0002333 92 0.02552 3 Genes involved in Mitotic Prometaphase www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_I_TRANSCRIPTION_INITIATION View Gene Set 0.0002374 24 0.02552 3 Genes involved in RNA PolymeraseTranscription Initiation www.broad.mit.e...
Broad REACTOME_CITRIC_ACID_CYCLE View Gene Set 0.000381 19 0.02602 5 Genes involved in Citric acid cycle (TCA cycle) www.broad.mit.e...
Broad REACTOME_ELECTRON_TRANSPORT_CHAIN View Gene Set 0.0004236 75 0.02602 5 Genes involved in Electron Transport Chain www.broad.mit.e...
Broad REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_COMPLEX View Gene Set 0.0004038 12 0.02602 5 Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_I_PROMOTER_ESCAPE View Gene Set 0.0005701 20 0.03064 8 Genes involved in RNA Polymerase I Promoter Escape 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_126 View Gene Set 7.891e-07 173 0.0003582 1 Genes in module_126 www.broad.mit.e...
Broad module_139 View Gene Set 0.0003203 74 0.04887 2 Genes in module_139 www.broad.mit.e...
Broad module_180 View Gene Set 0.0003843 113 0.04887 2 Genes in module_180 www.broad.mit.e...
Broad module_325 View Gene Set 0.0004305 46 0.04887 2 Genes in module_325 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 11780052 View Gene Set 4.489e-21 517 1.126e-17 1 The DNA sequence and comparative analysis of human chromosome 20. www.ncbi.nlm.ni...
PMID 15772651 View Gene Set 2.9e-14 397 3.635e-11 2 The DNA sequence of the human X chromosome. www.ncbi.nlm.ni...
PMID 11543634 View Gene Set 3.03e-05 58 0.02532 3 The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders. www.ncbi.nlm.ni...
PMID 15815621 View Gene Set 5.1e-05 437 0.03196 4 Generation and annotation of the DNA sequences of human chromosomes 2 and 4. www.ncbi.nlm.ni...

Gene Set Collection: ChromosomalTiles5Mb

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 chr19_10-15Mb View Gene Set 7.229e-16 87 8.054e-13 1 Genomic tile: chr19 ; 10000001-15000001 Mb genome.ucsc.edu...
Null chr8_142.5-147.5Mb View Gene Set 4.539e-13 64 2.499e-10 2 Genomic tile: chr8 ; 142500001-147500001 Mb genome.ucsc.edu...
Null chr8_145-150Mb View Gene Set 6.729e-13 33 2.499e-10 2 Genomic tile: chr8 ; 145000001-150000001 Mb genome.ucsc.edu...
Null chr19_7.5-12.5Mb View Gene Set 1.431e-09 79 3.984e-07 4 Genomic tile: chr19 ; 7500001-12500001 Mb genome.ucsc.edu...
Null chr20_32.5-37.5Mb View Gene Set 4.864e-09 53 1.084e-06 5 Genomic tile: chr20 ; 32500001-37500001 Mb genome.ucsc.edu...
Null chr19_12.5-17.5Mb View Gene Set 9.017e-09 85 1.674e-06 6 Genomic tile: chr19 ; 12500001-17500001 Mb genome.ucsc.edu...
Null chr19_60-65Mb View Gene Set 1.319e-08 70 2.099e-06 7 Genomic tile: chr19 ; 60000001-65000001 Mb genome.ucsc.edu...
Null chr19_55-60Mb View Gene Set 3.758e-08 85 5.233e-06 8 Genomic tile: chr19 ; 55000001-60000001 Mb genome.ucsc.edu...
Null chr3_97.5-102.5Mb View Gene Set 7.018e-08 16 8.686e-06 9 Genomic tile: chr3 ; 97500001-102500001 Mb genome.ucsc.edu...
Null chr17_72.5-77.5Mb View Gene Set 1.154e-07 77 1.169e-05 10 Genomic tile: chr17 ; 72500001-77500001 Mb genome.ucsc.edu...
Null chr19_57.5-62.5Mb View Gene Set 1.149e-07 70 1.169e-05 10 Genomic tile: chr19 ; 57500001-62500001 Mb genome.ucsc.edu...
Null chr20_30-35Mb View Gene Set 1.542e-07 51 1.431e-05 12 Genomic tile: chr20 ; 30000001-35000001 Mb genome.ucsc.edu...
Null chr19_62.5-67.5Mb View Gene Set 1.755e-07 35 1.504e-05 13 Genomic tile: chr19 ; 62500001-67500001 Mb genome.ucsc.edu...
Null chr3_12.5-17.5Mb View Gene Set 2.278e-07 35 1.812e-05 14 Genomic tile: chr3 ; 12500001-17500001 Mb genome.ucsc.edu...
Null chr8_95-100Mb View Gene Set 2.692e-07 26 1.999e-05 15 Genomic tile: chr8 ; 95000001-100000001 Mb genome.ucsc.edu...
Null chr8_97.5-102.5Mb View Gene Set 4.136e-07 24 2.88e-05 16 Genomic tile: chr8 ; 97500001-102500001 Mb genome.ucsc.edu...
Null chrX_115-120Mb View Gene Set 7.264e-07 23 4.76e-05 17 Genomic tile: chrX ; 115000001-120000001 Mb genome.ucsc.edu...
Null chr3_10-15Mb View Gene Set 1.273e-06 39 7.879e-05 18 Genomic tile: chr3 ; 10000001-15000001 Mb genome.ucsc.edu...
Null chr17_70-75Mb View Gene Set 1.501e-06 66 8.803e-05 19 Genomic tile: chr17 ; 70000001-75000001 Mb genome.ucsc.edu...
Null chr19_52.5-57.5Mb View Gene Set 2.232e-06 114 0.0001243 20 Genomic tile: chr19 ; 52500001-57500001 Mb genome.ucsc.edu...
Null chr2_97.5-102.5Mb View Gene Set 3.446e-06 25 0.0001745 21 Genomic tile: chr2 ; 97500001-102500001 Mb genome.ucsc.edu...
Null chr4_52.5-57.5Mb View Gene Set 3.402e-06 26 0.0001745 21 Genomic tile: chr4 ; 52500001-57500001 Mb genome.ucsc.edu...
Null chr19_5-10Mb View Gene Set 3.718e-06 67 0.0001801 23 Genomic tile: chr19 ; 5000001-10000001 Mb genome.ucsc.edu...
Null chr8_122.5-127.5Mb View Gene Set 3.892e-06 23 0.0001807 24 Genomic tile: chr8 ; 122500001-127500001 Mb genome.ucsc.edu...
Null chr3_100-105Mb View Gene Set 4.365e-06 15 0.000191 25 Genomic tile: chr3 ; 100000001-105000001 Mb genome.ucsc.edu...
Null chrX_147.5-152.5Mb View Gene Set 4.458e-06 55 0.000191 25 Genomic tile: chrX ; 147500001-152500001 Mb genome.ucsc.edu...
Null chr3_45-50Mb View Gene Set 5.757e-06 72 0.0002375 27 Genomic tile: chr3 ; 45000001-50000001 Mb genome.ucsc.edu...
Null chrX_117.5-122.5Mb View Gene Set 6.073e-06 18 0.0002416 28 Genomic tile: chrX ; 117500001-122500001 Mb genome.ucsc.edu...
Null chr19_15-20Mb View Gene Set 1.273e-05 98 0.00047 29 Genomic tile: chr19 ; 15000001-20000001 Mb genome.ucsc.edu...
Null chr19_17.5-22.5Mb View Gene Set 1.464e-05 66 0.00047 29 Genomic tile: chr19 ; 17500001-22500001 Mb genome.ucsc.edu...
Null chr1_0-5Mb View Gene Set 1.34e-05 50 0.00047 29 Genomic tile: chr1 ; 1-5000001 Mb genome.ucsc.edu...
Null chr1_222.5-227.5Mb View Gene Set 1.443e-05 40 0.00047 29 Genomic tile: chr1 ; 222500001-227500001 Mb genome.ucsc.edu...
Null chr2_110-115Mb View Gene Set 1.519e-05 31 0.00047 29 Genomic tile: chr2 ; 110000001-115000001 Mb genome.ucsc.edu...
Null chr3_120-125Mb View Gene Set 1.344e-05 45 0.00047 29 Genomic tile: chr3 ; 120000001-125000001 Mb genome.ucsc.edu...
Null chr3_47.5-52.5Mb View Gene Set 1.494e-05 94 0.00047 29 Genomic tile: chr3 ; 47500001-52500001 Mb genome.ucsc.edu...
Null chrX_45-50Mb View Gene Set 1.419e-05 58 0.00047 29 Genomic tile: chrX ; 45000001-50000001 Mb genome.ucsc.edu...
Null chr7_87.5-92.5Mb View Gene Set 1.67e-05 15 0.0005027 37 Genomic tile: chr7 ; 87500001-92500001 Mb genome.ucsc.edu...
Null chr3_95-100Mb View Gene Set 1.742e-05 10 0.0005108 38 Genomic tile: chr3 ; 95000001-100000001 Mb genome.ucsc.edu...
Null chr11_62.5-67.5Mb View Gene Set 2.072e-05 119 0.000592 39 Genomic tile: chr11 ; 62500001-67500001 Mb genome.ucsc.edu...
Null chrX_150-155Mb View Gene Set 2.156e-05 52 0.0006004 40 Genomic tile: chrX ; 150000001-155000001 Mb genome.ucsc.edu...
Null chr8_100-105Mb View Gene Set 3.066e-05 26 0.000833 41 Genomic tile: chr8 ; 100000001-105000001 Mb genome.ucsc.edu...
Null chr20_17.5-22.5Mb View Gene Set 3.611e-05 23 0.0009579 42 Genomic tile: chr20 ; 17500001-22500001 Mb genome.ucsc.edu...
Null chr20_22.5-27.5Mb View Gene Set 4.115e-05 20 0.001066 43 Genomic tile: chr20 ; 22500001-27500001 Mb genome.ucsc.edu...
Null chr11_65-70Mb View Gene Set 5.263e-05 90 0.001333 44 Genomic tile: chr11 ; 65000001-70000001 Mb genome.ucsc.edu...
Null chr10_35-40Mb View Gene Set 5.563e-05 10 0.001362 45 Genomic tile: chr10 ; 35000001-40000001 Mb genome.ucsc.edu...
Null chr2_100-105Mb View Gene Set 5.625e-05 18 0.001362 45 Genomic tile: chr2 ; 100000001-105000001 Mb genome.ucsc.edu...
Null chr4_152.5-157.5Mb View Gene Set 7.706e-05 26 0.001826 47 Genomic tile: chr4 ; 152500001-157500001 Mb genome.ucsc.edu...
Null chr19_20-25Mb View Gene Set 7.924e-05 14 0.001839 48 Genomic tile: chr19 ; 20000001-25000001 Mb genome.ucsc.edu...
Null chrX_130-135Mb View Gene Set 8.499e-05 23 0.001932 49 Genomic tile: chrX ; 130000001-135000001 Mb genome.ucsc.edu...
Null chr14_62.5-67.5Mb View Gene Set 9.653e-05 31 0.002151 50 Genomic tile: chr14 ; 62500001-67500001 Mb genome.ucsc.edu...
Null chr20_15-20Mb View Gene Set 0.0001061 22 0.002274 51 Genomic tile: chr20 ; 15000001-20000001 Mb genome.ucsc.edu...
Null chr2_95-100Mb View Gene Set 0.0001057 35 0.002274 51 Genomic tile: chr2 ; 95000001-100000001 Mb genome.ucsc.edu...
Null chr1_202.5-207.5Mb View Gene Set 0.0001122 40 0.002357 53 Genomic tile: chr1 ; 202500001-207500001 Mb genome.ucsc.edu...
Null chr1_205-210Mb View Gene Set 0.0001214 28 0.0025 54 Genomic tile: chr1 ; 205000001-210000001 Mb genome.ucsc.edu...
Null chr2_112.5-117.5Mb View Gene Set 0.0001234 26 0.0025 54 Genomic tile: chr2 ; 112500001-117500001 Mb genome.ucsc.edu...
Null chr8_125-130Mb View Gene Set 0.0001359 15 0.002703 56 Genomic tile: chr8 ; 125000001-130000001 Mb genome.ucsc.edu...
Null chr20_2.5-7.5Mb View Gene Set 0.0001575 33 0.003077 57 Genomic tile: chr20 ; 2500001-7500001 Mb genome.ucsc.edu...
Null chr11_125-130Mb View Gene Set 0.0001779 27 0.003417 58 Genomic tile: chr11 ; 125000001-130000001 Mb genome.ucsc.edu...
Null chr14_65-70Mb View Gene Set 0.0001923 27 0.003631 59 Genomic tile: chr14 ; 65000001-70000001 Mb genome.ucsc.edu...
Null chrX_42.5-47.5Mb View Gene Set 0.0002027 33 0.003763 60 Genomic tile: chrX ; 42500001-47500001 Mb genome.ucsc.edu...
Null chr11_122.5-127.5Mb View Gene Set 0.0002191 34 0.003936 61 Genomic tile: chr11 ; 122500001-127500001 Mb genome.ucsc.edu...
Null chr8_120-125Mb View Gene Set 0.0002189 21 0.003936 61 Genomic tile: chr8 ; 120000001-125000001 Mb genome.ucsc.edu...
Null chr4_150-155Mb View Gene Set 0.0002254 12 0.003985 63 Genomic tile: chr4 ; 150000001-155000001 Mb genome.ucsc.edu...
Null chr14_20-25Mb View Gene Set 0.000253 56 0.004404 64 Genomic tile: chr14 ; 20000001-25000001 Mb genome.ucsc.edu...
Null chr20_60-65Mb View Gene Set 0.0003154 44 0.005406 65 Genomic tile: chr20 ; 60000001-65000001 Mb genome.ucsc.edu...
Null chr2_117.5-122.5Mb View Gene Set 0.0003218 17 0.005432 66 Genomic tile: chr2 ; 117500001-122500001 Mb genome.ucsc.edu...
Null chr12_25-30Mb View Gene Set 0.0003888 20 0.006464 67 Genomic tile: chr12 ; 25000001-30000001 Mb genome.ucsc.edu...
Null chr3_117.5-122.5Mb View Gene Set 0.000405 21 0.006635 68 Genomic tile: chr3 ; 117500001-122500001 Mb genome.ucsc.edu...
Null chr2_127.5-132.5Mb View Gene Set 0.0005442 27 0.008787 69 Genomic tile: chr2 ; 127500001-132500001 Mb genome.ucsc.edu...
Null chr8_92.5-97.5Mb View Gene Set 0.0005605 21 0.00892 70 Genomic tile: chr8 ; 92500001-97500001 Mb genome.ucsc.edu...
Null chrX_7.5-12.5Mb View Gene Set 0.0006029 14 0.00946 71 Genomic tile: chrX ; 7500001-12500001 Mb genome.ucsc.edu...
Null chr20_25-30Mb View Gene Set 0.0006572 9 0.01017 72 Genomic tile: chr20 ; 25000001-30000001 Mb genome.ucsc.edu...
Null chr3_20-25Mb View Gene Set 0.0006937 9 0.01059 73 Genomic tile: chr3 ; 20000001-25000001 Mb genome.ucsc.edu...
Null chrX_12.5-17.5Mb View Gene Set 0.00072 23 0.01084 74 Genomic tile: chrX ; 12500001-17500001 Mb genome.ucsc.edu...
Null chr2_235-240Mb View Gene Set 0.0007702 18 0.01144 75 Genomic tile: chr2 ; 235000001-240000001 Mb genome.ucsc.edu...
Null chr20_35-40Mb View Gene Set 0.0008402 30 0.01232 76 Genomic tile: chr20 ; 35000001-40000001 Mb genome.ucsc.edu...
Null chr4_50-55Mb View Gene Set 0.0008698 11 0.01242 77 Genomic tile: chr4 ; 50000001-55000001 Mb genome.ucsc.edu...
Null chrX_5-10Mb View Gene Set 0.0008652 11 0.01242 77 Genomic tile: chrX ; 5000001-10000001 Mb genome.ucsc.edu...
Null chr8_77.5-82.5Mb View Gene Set 0.0008938 14 0.0126 79 Genomic tile: chr8 ; 77500001-82500001 Mb genome.ucsc.edu...
Null chr4_177.5-182.5Mb View Gene Set 0.0009268 7 0.01291 80 Genomic tile: chr4 ; 177500001-182500001 Mb genome.ucsc.edu...
Null chr2_167.5-172.5Mb View Gene Set 0.0009591 22 0.01319 81 Genomic tile: chr2 ; 167500001-172500001 Mb genome.ucsc.edu...
Null chr14_57.5-62.5Mb View Gene Set 0.001005 23 0.01349 82 Genomic tile: chr14 ; 57500001-62500001 Mb genome.ucsc.edu...
Null chr8_140-145Mb View Gene Set 0.0009993 40 0.01349 82 Genomic tile: chr8 ; 140000001-145000001 Mb genome.ucsc.edu...
Null chr1_2.5-7.5Mb View Gene Set 0.001023 33 0.01357 84 Genomic tile: chr1 ; 2500001-7500001 Mb genome.ucsc.edu...
Null chr2_120-125Mb View Gene Set 0.001058 17 0.01386 85 Genomic tile: chr2 ; 120000001-125000001 Mb genome.ucsc.edu...
Null chr2_102.5-107.5Mb View Gene Set 0.001155 13 0.01496 86 Genomic tile: chr2 ; 102500001-107500001 Mb genome.ucsc.edu...
Null chr1_212.5-217.5Mb View Gene Set 0.001346 12 0.01724 87 Genomic tile: chr1 ; 212500001-217500001 Mb genome.ucsc.edu...
Null chr8_117.5-122.5Mb View Gene Set 0.001508 15 0.01909 88 Genomic tile: chr8 ; 117500001-122500001 Mb genome.ucsc.edu...
Null chrX_112.5-117.5Mb View Gene Set 0.001576 13 0.01973 89 Genomic tile: chrX ; 112500001-117500001 Mb genome.ucsc.edu...
Null chrX_15-20Mb View Gene Set 0.001598 19 0.01978 90 Genomic tile: chrX ; 15000001-20000001 Mb genome.ucsc.edu...
Null chrX_132.5-137.5Mb View Gene Set 0.001629 17 0.01995 91 Genomic tile: chrX ; 132500001-137500001 Mb genome.ucsc.edu...
Null chr17_75-80Mb View Gene Set 0.001686 37 0.02041 92 Genomic tile: chr17 ; 75000001-80000001 Mb genome.ucsc.edu...
Null chr3_102.5-107.5Mb View Gene Set 0.001737 7 0.0208 93 Genomic tile: chr3 ; 102500001-107500001 Mb genome.ucsc.edu...
Null chr10_75-80Mb View Gene Set 0.001775 17 0.02082 94 Genomic tile: chr10 ; 75000001-80000001 Mb genome.ucsc.edu...
Null chr18_57.5-62.5Mb View Gene Set 0.001776 16 0.02082 94 Genomic tile: chr18 ; 57500001-62500001 Mb genome.ucsc.edu...
Null chr19_50-55Mb View Gene Set 0.00187 112 0.02135 96 Genomic tile: chr19 ; 50000001-55000001 Mb genome.ucsc.edu...
Null chrX_127.5-132.5Mb View Gene Set 0.001878 19 0.02135 96 Genomic tile: chrX ; 127500001-132500001 Mb genome.ucsc.edu...
Null chrX_65-70Mb View Gene Set 0.001869 23 0.02135 96 Genomic tile: chrX ; 65000001-70000001 Mb genome.ucsc.edu...
Null chr20_10-15Mb View Gene Set 0.002014 9 0.02266 99 Genomic tile: chr20 ; 10000001-15000001 Mb genome.ucsc.edu...
Null chr20_20-25Mb View Gene Set 0.002155 18 0.02401 100 Genomic tile: chr20 ; 20000001-25000001 Mb genome.ucsc.edu...
Null chr2_82.5-87.5Mb View Gene Set 0.002256 28 0.02489 101 Genomic tile: chr2 ; 82500001-87500001 Mb genome.ucsc.edu...
Null chr3_15-20Mb View Gene Set 0.002359 20 0.02577 102 Genomic tile: chr3 ; 15000001-20000001 Mb genome.ucsc.edu...
Null chrX_105-110Mb View Gene Set 0.002419 19 0.02616 103 Genomic tile: chrX ; 105000001-110000001 Mb genome.ucsc.edu...
Null chr8_115-120Mb View Gene Set 0.002449 6 0.02624 104 Genomic tile: chr8 ; 115000001-120000001 Mb genome.ucsc.edu...
Null chr20_27.5-32.5Mb View Gene Set 0.002522 21 0.02675 105 Genomic tile: chr20 ; 27500001-32500001 Mb genome.ucsc.edu...
Null chr4_55-60Mb View Gene Set 0.002623 20 0.02756 106 Genomic tile: chr4 ; 55000001-60000001 Mb genome.ucsc.edu...
Null chr10_70-75Mb View Gene Set 0.002926 54 0.03046 107 Genomic tile: chr10 ; 70000001-75000001 Mb genome.ucsc.edu...
Null chr1_220-225Mb View Gene Set 0.003188 28 0.03288 108 Genomic tile: chr1 ; 220000001-225000001 Mb genome.ucsc.edu...
Null chr10_37.5-42.5Mb View Gene Set 0.003576 7 0.03591 109 Genomic tile: chr10 ; 37500001-42500001 Mb genome.ucsc.edu...
Null chr3_35-40Mb View Gene Set 0.003578 24 0.03591 109 Genomic tile: chr3 ; 35000001-40000001 Mb genome.ucsc.edu...
Null chr8_107.5-112.5Mb View Gene Set 0.003537 9 0.03591 109 Genomic tile: chr8 ; 107500001-112500001 Mb genome.ucsc.edu...
Null chr5_172.5-177.5Mb View Gene Set 0.003617 36 0.03597 112 Genomic tile: chr5 ; 172500001-177500001 Mb genome.ucsc.edu...
Null chr11_45-50Mb View Gene Set 0.003693 35 0.03641 113 Genomic tile: chr11 ; 45000001-50000001 Mb genome.ucsc.edu...
Null chr3_7.5-12.5Mb View Gene Set 0.003974 42 0.03883 114 Genomic tile: chr3 ; 7500001-12500001 Mb genome.ucsc.edu...
Null chr2_92.5-97.5Mb View Gene Set 0.004024 21 0.03898 115 Genomic tile: chr2 ; 92500001-97500001 Mb genome.ucsc.edu...
Null chr8_87.5-92.5Mb View Gene Set 0.004153 13 0.03989 116 Genomic tile: chr8 ; 87500001-92500001 Mb genome.ucsc.edu...
Null chr1_200-205Mb View Gene Set 0.004245 57 0.04041 117 Genomic tile: chr1 ; 200000001-205000001 Mb genome.ucsc.edu...
Null chr14_55-60Mb View Gene Set 0.004513 27 0.04261 118 Genomic tile: chr14 ; 55000001-60000001 Mb genome.ucsc.edu...
Null chr4_82.5-87.5Mb View Gene Set 0.004564 13 0.04272 119 Genomic tile: chr4 ; 82500001-87500001 Mb genome.ucsc.edu...
Null chr10_72.5-77.5Mb View Gene Set 0.004678 42 0.04343 120 Genomic tile: chr10 ; 72500001-77500001 Mb genome.ucsc.edu...
Null chr11_60-65Mb View Gene Set 0.004925 104 0.04513 121 Genomic tile: chr11 ; 60000001-65000001 Mb genome.ucsc.edu...
Null chr2_170-175Mb View Gene Set 0.004942 30 0.04513 121 Genomic tile: chr2 ; 170000001-175000001 Mb genome.ucsc.edu...
Null chr11_0-5Mb View Gene Set 0.005102 69 0.04584 123 Genomic tile: chr11 ; 1-5000001 Mb genome.ucsc.edu...
Null chr20_57.5-62.5Mb View Gene Set 0.00508 38 0.04584 123 Genomic tile: chr20 ; 57500001-62500001 Mb genome.ucsc.edu...
Null chr10_60-65Mb View Gene Set 0.005237 11 0.04597 125 Genomic tile: chr10 ; 60000001-65000001 Mb genome.ucsc.edu...
Null chr11_42.5-47.5Mb View Gene Set 0.00524 38 0.04597 125 Genomic tile: chr11 ; 42500001-47500001 Mb genome.ucsc.edu...
Null chr2_215-220Mb View Gene Set 0.005189 36 0.04597 125 Genomic tile: chr2 ; 215000001-220000001 Mb genome.ucsc.edu...
Null chr11_117.5-122.5Mb View Gene Set 0.005453 48 0.04746 128 Genomic tile: chr11 ; 117500001-122500001 Mb genome.ucsc.edu...
Null chr3_110-115Mb View Gene Set 0.00557 25 0.0481 129 Genomic tile: chr3 ; 110000001-115000001 Mb genome.ucsc.edu...

Gene Set Collection: Prosite

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 PS50805 View Gene Set 8.833e-07 415 0.0006492 1 KRAB expasy.org/pros...
Null PS00322 View Gene Set 0.000114 19 0.02794 2 HISTONE_H3_1 expasy.org/pros...
Null PS00959 View Gene Set 9.747e-05 21 0.02794 2 HISTONE_H3_2 expasy.org/pros...

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 RNA Polymerase I Promoter Clearance View Gene Set 4.688e-08 55 3.416e-05 1 REACTOME - RNA Polymerase I Promoter Clearance gene set www.pathwaycomm...
Null RNA Polymerase I Chain Elongation View Gene Set 6.116e-08 49 3.416e-05 1 REACTOME - RNA Polymerase I Chain Elongation gene set www.pathwaycomm...
Null RNA Polymerase I Transcription View Gene Set 1.046e-07 57 3.895e-05 3 REACTOME - RNA Polymerase I Transcription gene set www.pathwaycomm...
Null RNA Polymerase I RNA Polymerase III and Mitochondrial Transcription View Gene Set 2.531e-07 93 7.067e-05 4 REACTOME - RNA Polymerase I RNA Polymerase III and Mitochondrial Transcription gene set www.pathwaycomm... RNA Polymerase ... and Mitochondri...
Null RNA Polymerase I Promoter Opening View Gene Set 1.853e-05 31 0.004141 5 REACTOME - RNA Polymerase I Promoter Opening gene set www.pathwaycomm...
Null Pyruvate metabolism and Citric Acid (TCA) cycle View Gene Set 9.032e-05 31 0.01681 6 REACTOME - Pyruvate metabolism and Citric Acid (TCA) cycle gene set www.pathwaycomm...
Null Mitotic Prometaphase View Gene Set 0.0001161 86 0.01852 7 REACTOME - Mitotic Prometaphase gene set www.pathwaycomm...
Null Activation of DNA fragmentation factor View Gene Set 0.000242 8 0.02253 8 REACTOME - Activation of DNA fragmentation factor gene set www.pathwaycomm...
Null Apoptosis induced DNA fragmentation View Gene Set 0.000242 8 0.02253 8 REACTOME - Apoptosis induced DNA fragmentation gene set www.pathwaycomm...
Null RNA Polymerase I Transcription Initiation View Gene Set 0.0002374 25 0.02253 8 REACTOME - RNA Polymerase I Transcription Initiation gene set www.pathwaycomm...
Null Transcription View Gene Set 0.0001743 178 0.02253 8 REACTOME - Transcription gene set www.pathwaycomm...
Null M Phase View Gene Set 0.0002278 90 0.02253 8 REACTOME - M Phase gene set www.pathwaycomm...
Null Citric acid cycle (TCA cycle) View Gene Set 0.000381 19 0.03274 13 REACTOME - Citric acid cycle (TCA cycle) gene set www.pathwaycomm...
Null Respiratory electron transport View Gene Set 0.0004236 76 0.0338 14 REACTOME - Respiratory electron transport gene set www.pathwaycomm...
Null RNA Polymerase I Promoter Escape View Gene Set 0.0005701 21 0.04246 15 REACTOME - RNA Polymerase I Promoter Escape 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-596 View Gene Set 2.683e-05 644 0.009539 1 microRNA targets for hsa-miR-596 from mirbase.targets www.mirbase.org...
Null hsa-miR-941 View Gene Set 2.667e-05 590 0.009539 1 microRNA targets for hsa-miR-941 from mirbase.targets www.mirbase.org...
Null hsa-miR-663 View Gene Set 9.308e-05 743 0.02206 3 microRNA targets for hsa-miR-663 from mirbase.targets www.mirbase.org...
Null hsa-miR-127-3p View Gene Set 0.0001909 653 0.02357 4 microRNA targets for hsa-miR-127-3p from mirbase.targets www.mirbase.org...
Null hsa-miR-486-3p View Gene Set 0.0001989 773 0.02357 4 microRNA targets for hsa-miR-486-3p from mirbase.targets www.mirbase.org...
Null hsa-miR-593 View Gene Set 0.0001344 556 0.02357 4 microRNA targets for hsa-miR-593 from mirbase.targets www.mirbase.org...
Null hsa-miR-296-5p View Gene Set 0.0002638 755 0.02679 7 microRNA targets for hsa-miR-296-5p from mirbase.targets www.mirbase.org...

Gene Set Collection: hprdBatch.DIFFERENT

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 IL-1 Signaling Pathway View Gene Set 0.002138 233 0.04275 1 From NetPath for IL-1 Signaling Pathway www.netpath.org...