Results

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Go to: Gene Set Collection: KEGG
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Go to: Gene Set Collection: Broad.c2.CP.KEGG
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Go to: Gene Set Collection: Broad.c5.MF
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Go to: Gene Set Collection: pathwayCommons.reactome
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Go to: Gene Set Collection: hprdBatch.DOWN
Go to: Gene Set Collection: hprdManual.UP

AFA results for: VPA5e05.ls

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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 5.464e-05 1120 0.01169 1 Metabolic pathways www.genome.jp/d...
KEGG 00982 View Gene Set 0.0002278 73 0.0243 2 Drug metabolism - cytochrome P450 www.genome.jp/d...
KEGG 04146 View Gene Set 0.0003407 78 0.0243 2 Peroxisome www.genome.jp/d...
KEGG 00480 View Gene Set 0.0006015 50 0.02575 4 Glutathione metabolism www.genome.jp/d...
KEGG 00980 View Gene Set 0.0005606 71 0.02575 4 Metabolism of xenobiotics by cytochrome P450 www.genome.jp/d...
KEGG 04142 View Gene Set 0.000994 121 0.03545 6 Lysosome 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 1.207e-09 5184 1.612e-05 1 cytoplasmic part amigo.geneontol...
GO GO:0005739 View Gene Set 2.119e-08 1274 0.0001416 2 mitochondrion amigo.geneontol...
GO GO:0055114 View Gene Set 1.238e-07 647 0.0005511 3 oxidation reduction amigo.geneontol...
GO GO:0016491 View Gene Set 3.499e-07 689 0.001169 4 oxidoreductase activity amigo.geneontol...
GO GO:0005737 View Gene Set 2.324e-06 7676 0.00621 5 cytoplasm amigo.geneontol...
GO GO:0003824 View Gene Set 4.29e-06 5198 0.009552 6 catalytic activity amigo.geneontol...
GO GO:0006082 View Gene Set 1.705e-05 620 0.02847 7 organic acid metabolic process amigo.geneontol...
GO GO:0016614 View Gene Set 1.628e-05 115 0.02847 7 oxidoreductase activity acting on CH-OH group of donors 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 chr17p11 View Gene Set 7.72e-06 118 0.002517 1 Genes in cytogenetic band chr17p11 www.broad.mit.e...
Broad chr14q11 View Gene Set 2.014e-05 289 0.003284 2 Genes in cytogenetic band chr14q11 www.broad.mit.e...
Broad chr21q22 View Gene Set 7.139e-05 192 0.007758 3 Genes in cytogenetic band chr21q22 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 ONDER_CDH1_TARGETS_2_DN View Gene Set 5.464e-23 453 1.307e-19 1 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 COLDREN_GEFITINIB_RESISTANCE_DN View Gene Set 3.708e-16 217 4.435e-13 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 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP View Gene Set 1.572e-10 114 1.253e-07 3 Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. www.broad.mit.e...
Broad BROWNE_INTERFERON_RESPONSIVE_GENES View Gene Set 1.602e-09 67 9.579e-07 4 Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP View Gene Set 1.725e-08 422 8.251e-06 5 Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. www.broad.mit.e...
Broad MOSERLE_IFNA_RESPONSE View Gene Set 2.867e-08 30 9.795e-06 6 Top 50 genes up-regulated in ovarian cancer progenitor cells (also known as side population SP cells) in response to interferon alpha (IFNA). www.broad.mit.e...
Broad CHANG_IMMORTALIZED_BY_HPV31_DN View Gene Set 2.81e-08 47 9.795e-06 6 Genes down-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. www.broad.mit.e...
Broad MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN View Gene Set 5.933e-08 317 1.774e-05 8 The postradiation tumor escape signature: genes down-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. www.broad.mit.e...
Broad BASAKI_YBX1_TARGETS_DN View Gene Set 8.158e-08 356 1.978e-05 9 Genes down-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [Gene ID=4904] knockdown by RNAi. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP View Gene Set 8.271e-08 716 1.978e-05 9 Genes up-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 DELYS_THYROID_CANCER_UP View Gene Set 1.737e-07 397 3.778e-05 11 Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. www.broad.mit.e...
Broad CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 View Gene Set 3.502e-07 681 6.981e-05 12 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 DAUER_STAT3_TARGETS_DN View Gene Set 4.696e-07 37 8.641e-05 13 Top 50 genes down-regulated in A549 cells (lung cancer) expressing STAT3 [Gene ID=6774] off an adenovirus vector. www.broad.mit.e...
Broad SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN View Gene Set 6.445e-07 571 0.0001101 14 Genes down-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. www.broad.mit.e...
Broad GALE_APL_WITH_FLT3_MUTATED_DN View Gene Set 2.821e-06 17 0.0004499 15 Genes down-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [Gene ID=2322]. www.broad.mit.e...
Broad RODRIGUES_DCC_TARGETS_DN View Gene Set 3.703e-06 121 0.0004921 16 Genes down-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [Gene ID=9423] compared to those stably expressing wild type DCC off a plasmid vector. www.broad.mit.e...
Broad BOWIE_RESPONSE_TO_TAMOXIFEN View Gene Set 3.346e-06 14 0.0004921 16 Genes up-regulated by tamoxifen [PubChem=5376] in HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [Gene ID=1489078]). www.broad.mit.e...
Broad WU_CELL_MIGRATION View Gene Set 3.585e-06 182 0.0004921 16 Genes associated with migration rate of 40 human bladder cancer cells. www.broad.mit.e...
Broad ZHANG_INTERFERON_RESPONSE View Gene Set 4.254e-06 21 0.0005355 19 Interferon-inducible genes up-regulated in A549 cells (lung cancer) infected with a respiratory syncytial virus (RSV) that had its NS1 [Gene ID=1494468] gene knocked down by RNAi. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN View Gene Set 4.859e-06 155 0.0005811 20 Marker genes down-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. www.broad.mit.e...
Broad EINAV_INTERFERON_SIGNATURE_IN_CANCER View Gene Set 6.045e-06 27 0.0006885 21 A gene expression signature found in a subset of cancer patients suggestive of a deregulated immune or inflammatory response. www.broad.mit.e...
Broad UROSEVIC_RESPONSE_TO_IMIQUIMOD View Gene Set 8.556e-06 16 0.0009303 22 Interferon cluster genes up-regulated in skin tumors treated with imiquimod [PubChem=57469]. www.broad.mit.e...
Broad TSAI_DNAJB4_TARGETS_UP View Gene Set 9.03e-06 13 0.0009391 23 Genes up-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [Gene ID=11080] off a plasmid vector. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP View Gene Set 1.061e-05 869 0.001058 24 Genes up-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 AIGNER_ZEB1_TARGETS View Gene Set 1.153e-05 29 0.001061 25 Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [Gene ID=6935] by RNAi. www.broad.mit.e...
Broad BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS View Gene Set 1.144e-05 23 0.001061 25 Genes significantly up-regulated in the blood mononuclear cells from patients with systemic lupus erythematosus compared to those from healthy persons. www.broad.mit.e...
Broad SANA_TNF_SIGNALING_UP View Gene Set 1.249e-05 75 0.001106 27 Genes up-regulated in five primary endothelial cell types (lung aortic iliac dermal and colon) by TNF [Gene ID=7124]. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN View Gene Set 1.786e-05 437 0.001526 28 Genes down-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. www.broad.mit.e...
Broad BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX View Gene Set 2.079e-05 10 0.001715 29 Genes up-regulated by growing HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [Gene ID=1489078]) in extracellular matrix (ECM). www.broad.mit.e...
Broad TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP View Gene Set 3.147e-05 182 0.002509 30 Genes up-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [Gene ID=861 862] fusion. www.broad.mit.e...
Broad SEKI_INFLAMMATORY_RESPONSE_LPS_UP View Gene Set 4.69e-05 75 0.003619 31 Genes up-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). www.broad.mit.e...
Broad STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN View Gene Set 5.287e-05 437 0.003832 32 Genes down-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. www.broad.mit.e...
Broad MOOTHA_MITOCHONDRIA View Gene Set 5.153e-05 433 0.003832 32 Mitochondrial genes www.broad.mit.e...
Broad JAEGER_METASTASIS_DN View Gene Set 8.072e-05 252 0.005081 34 Genes down-regulated in metastases from malignant melanoma compared to the primary tumors. www.broad.mit.e...
Broad ENK_UV_RESPONSE_KERATINOCYTE_UP View Gene Set 7.973e-05 517 0.005081 34 Genes up-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. www.broad.mit.e...
Broad LE_EGR2_TARGETS_DN View Gene Set 7.784e-05 100 0.005081 34 Genes down-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [Gene ID=1959]. www.broad.mit.e...
Broad KIM_LRRC3B_TARGETS View Gene Set 7.825e-05 30 0.005081 34 Immune response genes up-regulated in zenograft tumors formed by SNU-601 cells (gastric cancer) made to express LRRC3B [Gene ID=116135]. www.broad.mit.e...
Broad MASSARWEH_TAMOXIFEN_RESISTANCE_UP View Gene Set 7.428e-05 531 0.005081 34 Genes up-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. www.broad.mit.e...
Broad SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN View Gene Set 9.216e-05 296 0.005511 39 Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. www.broad.mit.e...
Broad FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN View Gene Set 9.025e-05 431 0.005511 39 Genes down-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin LGALS1) [Gene ID=3956] compared to that with bacterial lipopolysaccharide (LPS). www.broad.mit.e...
Broad MOOTHA_HUMAN_MITODB_6_2002 View Gene Set 0.0001031 420 0.006016 41 Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad ALCALA_APOPTOSIS View Gene Set 0.0001063 87 0.006052 42 Genes able to induce cell death in an expression cDNA library screen. www.broad.mit.e...
Broad DODD_NASOPHARYNGEAL_CARCINOMA_UP View Gene Set 0.0001215 1582 0.00632 43 Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. www.broad.mit.e...
Broad LANDIS_BREAST_CANCER_PROGRESSION_UP View Gene Set 0.000114 42 0.00632 43 Genes up-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. www.broad.mit.e...
Broad SANA_RESPONSE_TO_IFNG_UP View Gene Set 0.0001172 68 0.00632 43 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 HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN View Gene Set 0.0001199 70 0.00632 43 Genes down-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [Gene ID=3205 4211]. www.broad.mit.e...
Broad GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP View Gene Set 0.0001454 38 0.007244 47 Genes up-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [Gene ID=6223]. www.broad.mit.e...
Broad FURUKAWA_DUSP6_TARGETS_PCI35_UP View Gene Set 0.0001449 64 0.007244 47 Genes up-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 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP View Gene Set 0.0001687 20 0.008237 49 Genes up-regulated by RUNX1-RUNX1T1 [Gene ID=861 862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. www.broad.mit.e...
Broad CAIRO_LIVER_DEVELOPMENT_DN View Gene Set 0.0002183 208 0.01044 50 Genes down-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). www.broad.mit.e...
Broad THUM_SYSTOLIC_HEART_FAILURE_UP View Gene Set 0.0002368 393 0.0105 51 Genes up-regulated in samples with systolic heart failure compared to normal hearts. www.broad.mit.e...
Broad NUYTTEN_NIPP1_TARGETS_UP View Gene Set 0.0002311 657 0.0105 51 Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [Gene ID=5511] by RNAi. www.broad.mit.e...
Broad WELCSH_BRCA1_TARGETS_1_UP View Gene Set 0.000237 171 0.0105 51 Upregulated by induction of exogenous BRCA1 in EcR-293 cells www.broad.mit.e...
Broad JI_RESPONSE_TO_FSH_UP View Gene Set 0.0002311 54 0.0105 51 Genes up-regulated in MCV152 cells (ovarian cancer) treated with follicle stimulating hormone (FSH). www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP View Gene Set 0.0002449 174 0.01065 55 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 3 days after transduction. www.broad.mit.e...
Broad LIANG_SILENCED_BY_METHYLATION_2 View Gene Set 0.0002495 35 0.01066 56 Genes up-regulated in T24 cells (bladder carcinoma) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. www.broad.mit.e...
Broad JISON_SICKLE_CELL_DISEASE_UP View Gene Set 0.0002626 175 0.01102 57 Genes up-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. www.broad.mit.e...
Broad LINDSTEDT_DENDRITIC_CELL_MATURATION_A View Gene Set 0.0002731 54 0.01126 58 Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 8 hr after the stimulation (cluster A). www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP View Gene Set 0.0002899 186 0.01137 59 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 10 days after transduction. www.broad.mit.e...
Broad LANDIS_ERBB2_BREAST_TUMORS_324_UP View Gene Set 0.0002884 132 0.01137 59 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 KIM_MYCN_AMPLIFICATION_TARGETS_DN View Gene Set 0.00029 78 0.01137 59 Genes negatively correlated with amplifications of MYCN [Gene ID=4613] in the SCLC (small cell lung cancer) cell lines. www.broad.mit.e...
Broad SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP View Gene Set 0.0003518 72 0.01351 62 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 ROZANOV_MMP14_TARGETS_UP View Gene Set 0.000358 260 0.01351 62 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 WANG_CISPLATIN_RESPONSE_AND_XPC_UP View Gene Set 0.0003616 135 0.01351 62 Genes up-regulated in fibroblasts with defective XPC [Gene ID=7508] in response to cisplatin [PubChem=2767]. www.broad.mit.e...
Broad SMID_BREAST_CANCER_BASAL_DN View Gene Set 0.0003761 664 0.01384 65 Genes down-regulated in basal subtype of breast cancer samles. www.broad.mit.e...
Broad RUIZ_TNC_TARGETS_UP View Gene Set 0.000388 145 0.01406 66 Genes up-regulated in T98G cells (glioblastoma) by TNC [Gene ID=3371]. www.broad.mit.e...
Broad MAHADEVAN_RESPONSE_TO_MP470_UP View Gene Set 0.0004449 19 0.01572 67 Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] after treatment with MP470 a protein kinase inhibitor. www.broad.mit.e...
Broad KOBAYASHI_EGFR_SIGNALING_24HR_UP View Gene Set 0.0004469 96 0.01572 67 Genes up-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 BRUECKNER_TARGETS_OF_MIRLET7A3_UP View Gene Set 0.0005035 105 0.01746 69 Genes up-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [Gene ID=406883] microRNA off a plasmid vector. www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_UP View Gene Set 0.0005412 163 0.01849 70 Genes up-regulated in MCF7 cells (breast cancer) under hypoxia conditions. www.broad.mit.e...
Broad BILD_HRAS_ONCOGENIC_SIGNATURE View Gene Set 0.0005874 248 0.01979 71 Genes selected in supervised analyses to discriminate cells expressing activated HRAS [Gene ID=3265] oncogene from control cells expressing GFP. www.broad.mit.e...
Broad SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 View Gene Set 0.0005995 407 0.01992 72 Genes up-regulated in the pancreatic cancer cell lines (AsPC1 Hs766T MiaPaCa2 Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. www.broad.mit.e...
Broad DOANE_BREAST_CANCER_ESR1_UP View Gene Set 0.0006728 104 0.02179 73 Genes changed in breast cancer samples according to the ESR1 [Gene ID=2099] status: ER positive vs ER negative tumors. www.broad.mit.e...
Broad NUYTTEN_EZH2_TARGETS_UP View Gene Set 0.0006744 944 0.02179 73 Genes up-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [Gene ID=2146] by RNAi. www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13 View Gene Set 0.0006832 158 0.02179 73 Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 13. www.broad.mit.e...
Broad DER_IFN_ALPHA_RESPONSE_UP View Gene Set 0.000716 57 0.02224 76 Genes up-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. www.broad.mit.e...
Broad ROETH_TERT_TARGETS_UP View Gene Set 0.0007154 8 0.02224 76 Genes up-regulated in T lymphocytes overexpressing TERT [Gene ID=7015] off a retrovirus vector. www.broad.mit.e...
Broad HOSHIDA_LIVER_CANCER_SUBCLASS_S3 View Gene Set 0.000751 266 0.02253 78 Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 View Gene Set 0.0007437 68 0.02253 78 Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 9. www.broad.mit.e...
Broad ZHAN_MULTIPLE_MYELOMA_HP_UP View Gene Set 0.0007536 44 0.02253 78 Top 50 up-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. www.broad.mit.e...
Broad BECKER_TAMOXIFEN_RESISTANCE_UP View Gene Set 0.0008016 38 0.02367 81 Genes up-regulated in a breast cancer cell line resistant to tamoxifen [PubChem ID=5376] compared to the parental line sensitive to the drug. www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP View Gene Set 0.0008188 153 0.02389 82 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 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 View Gene Set 0.0008545 23 0.02463 83 Cluster 5: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516 5352]. www.broad.mit.e...
Broad ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP View Gene Set 0.001031 78 0.02833 84 Genes up-regulated in P493-6 cells (B lymphocyte) by MYC [Gene ID=4609] and down-regulated by RNAi knockdown of TFRC [Gene ID=7037]. www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_BY_DMOG_UP View Gene Set 0.001027 125 0.02833 84 Genes up-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. www.broad.mit.e...
Broad MARKS_HDAC_TARGETS_UP View Gene Set 0.001056 21 0.02833 84 Genes whose transcription is altered by histone deacetylase inhibitors. www.broad.mit.e...
Broad ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP View Gene Set 0.001033 208 0.02833 84 Genes up-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [Gene ID=7124] or IKI-1 an inhibitor of I?B kinase (IKK). www.broad.mit.e...
Broad ONDER_CDH1_TARGETS_1_UP View Gene Set 0.001041 131 0.02833 84 Genes up-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 RADAEVA_RESPONSE_TO_IFNA1_UP View Gene Set 0.001056 32 0.02833 84 Genes up-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [Gene ID=3439]. www.broad.mit.e...
Broad KRASNOSELSKAYA_ILF3_TARGETS_UP View Gene Set 0.001066 31 0.02833 84 Up-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [Gene ID=3609]. www.broad.mit.e...
Broad GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3 View Gene Set 0.001125 11 0.02925 91 Genes up-regulated in Jurkat cells (T lymphocyte) by IFN1@ and IFNB1 [Gene ID=3438 3456] but not by overexpression of a constitutively active form of IRF3 [Gene ID=3661]. www.broad.mit.e...
Broad HINATA_NFKB_TARGETS_KERATINOCYTE_UP View Gene Set 0.001119 71 0.02925 91 Genes up-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [Gene ID=4790 5970] components of NFKB. www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS_UP View Gene Set 0.001173 368 0.03018 93 Genes up-regulated by ESRRA [Gene ID=2101] only. www.broad.mit.e...
Broad KORKOLA_YOLK_SAC_TUMOR View Gene Set 0.00126 49 0.03206 94 Genes predicting the yolk sac tumor (YS) subtype of nonseminomatous male germ cell tumors (NSGCT). www.broad.mit.e...
Broad PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN View Gene Set 0.001275 140 0.0321 95 Genes down-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. www.broad.mit.e...
Broad FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN View Gene Set 0.001299 532 0.03237 96 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 MISSIAGLIA_REGULATED_BY_METHYLATION_UP View Gene Set 0.001313 99 0.03238 97 Genes up-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 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN View Gene Set 0.001349 8 0.03293 98 Genes down-regulated by RUNX1-RUNX1T1 [Gene ID=861 862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. www.broad.mit.e...
Broad ONDER_CDH1_SIGNALING_VIA_CTNNB1 View Gene Set 0.001408 81 0.03402 99 Genes changed in HMLE cells (mmortalized nontransformed mammary epithelium) after RNAi knockdown of both CDH1 [Gene ID=999] and CTNNB1 [Gene ID=1499] compared to the knockdown of CDH1 alone. www.broad.mit.e...
Broad GAJATE_RESPONSE_TO_TRABECTEDIN_UP View Gene Set 0.001587 53 0.03796 100 Genes up-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. www.broad.mit.e...
Broad BASSO_CD40_SIGNALING_UP View Gene Set 0.001611 100 0.03816 101 Gene changed by CD40 [Gene ID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). www.broad.mit.e...
Broad THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP View Gene Set 0.001653 76 0.03876 102 Genes up-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. www.broad.mit.e...
Broad HOOI_ST7_TARGETS_DN View Gene Set 0.001717 108 0.03988 103 Genes down-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [Gene ID=7982] off a plasmid vector. www.broad.mit.e...
Broad NEWMAN_ERCC6_TARGETS_UP View Gene Set 0.001852 25 0.0426 104 Genes up-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [Gene ID=2074] off a plasmid vector. www.broad.mit.e...
Broad WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP View Gene Set 0.001986 131 0.0444 105 Genes up-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. www.broad.mit.e...
Broad YANAGIHARA_ESX1_TARGETS View Gene Set 0.001972 23 0.0444 105 Genes down-regulated in U2-OS Tet-On cells (osteosarcoma) after induction of ESX1 [Gene ID=80712] expression. www.broad.mit.e...
Broad WIELAND_UP_BY_HBV_INFECTION View Gene Set 0.001958 98 0.0444 105 Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. www.broad.mit.e...
Broad TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN View Gene Set 0.002084 52 0.04616 108 Genes down-regulated in monocytes by RUNX1-RUNX1T1 [Gene ID=861 862] fusion. www.broad.mit.e...
Broad TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP View Gene Set 0.002165 43 0.0475 109 Genes up-regulated by RUNX1-RUNX1T1 [Gene ID=861 862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing erythroid lineage. www.broad.mit.e...
Broad SENESE_HDAC3_TARGETS_UP View Gene Set 0.002223 471 0.04835 110 Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [Gene ID=8841] by RNAi. www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.BIOCARTA

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 BIOCARTA_IL10_PATHWAY View Gene Set 0.0004006 17 0.04347 1 IL-10 Anti-inflammatory Signaling Pathway www.broad.mit.e...
Broad BIOCARTA_RB_PATHWAY View Gene Set 0.0002138 13 0.04347 1 RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage 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_GLUTATHIONE_METABOLISM View Gene Set 0.0006015 50 0.02797 1 Glutathione metabolism www.broad.mit.e...
Broad KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 View Gene Set 0.0005606 70 0.02797 1 Metabolism of xenobiotics by cytochrome P450 www.broad.mit.e...
Broad KEGG_DRUG_METABOLISM_CYTOCHROME_P450 View Gene Set 0.0002278 72 0.02797 1 Drug metabolism - cytochrome P450 www.broad.mit.e...
Broad KEGG_PEROXISOME View Gene Set 0.0003407 78 0.02797 1 Peroxisome www.broad.mit.e...
Broad KEGG_LYSOSOME View Gene Set 0.000994 122 0.03698 5 Lysosome 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_CEBPA View Gene Set 0.0002983 64 0.04246 1 Neighborhood of CEBPA www.broad.mit.e...
Broad GNF2_CYP2B6 View Gene Set 0.0001192 49 0.04246 1 Neighborhood of CYP2B6 www.broad.mit.e...
Broad GNF2_EIF3S6 View Gene Set 0.0002894 109 0.04246 1 Neighborhood of EIF3S6 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_93 View Gene Set 6.753e-09 180 3.066e-06 1 Genes in module_93 www.broad.mit.e...
Broad module_114 View Gene Set 3.734e-05 314 0.005651 2 Genes in module_114 www.broad.mit.e...
Broad module_151 View Gene Set 3.031e-05 297 0.005651 2 Genes in module_151 www.broad.mit.e...
Broad module_86 View Gene Set 0.0002321 43 0.02108 4 Genes in module_86 www.broad.mit.e...
Broad module_180 View Gene Set 0.000217 113 0.02108 4 Genes in module_180 www.broad.mit.e...
Broad module_26 View Gene Set 0.0006474 178 0.02682 6 Genes in module_26 www.broad.mit.e...
Broad module_87 View Gene Set 0.0004848 44 0.02682 6 Genes in module_87 www.broad.mit.e...
Broad module_144 View Gene Set 0.0007772 8 0.02682 6 Genes in module_144 www.broad.mit.e...
Broad module_249 View Gene Set 0.0006752 21 0.02682 6 Genes in module_249 www.broad.mit.e...
Broad module_286 View Gene Set 0.000575 37 0.02682 6 Genes in module_286 www.broad.mit.e...
Broad module_327 View Gene Set 0.0005845 21 0.02682 6 Genes in module_327 www.broad.mit.e...
Broad module_357 View Gene Set 0.0007749 78 0.02682 6 Genes in module_357 www.broad.mit.e...
Broad module_431 View Gene Set 0.000609 15 0.02682 6 Genes in module_431 www.broad.mit.e...
Broad module_432 View Gene Set 0.0008269 15 0.02682 6 Genes in module_432 www.broad.mit.e...
Broad module_83 View Gene Set 0.0009066 296 0.02744 15 Genes in module_83 www.broad.mit.e...
Broad module_6 View Gene Set 0.001219 403 0.03257 16 Genes in module_6 www.broad.mit.e...
Broad module_172 View Gene Set 0.001177 93 0.03257 16 Genes in module_172 www.broad.mit.e...
Broad module_101 View Gene Set 0.001367 10 0.03447 18 Genes in module_101 www.broad.mit.e...
Broad module_29 View Gene Set 0.001715 28 0.04098 19 Genes in module_29 www.broad.mit.e...
Broad module_132 View Gene Set 0.002077 13 0.04436 20 Genes in module_132 www.broad.mit.e...
Broad module_212 View Gene Set 0.002141 316 0.04436 20 Genes in module_212 www.broad.mit.e...
Broad module_297 View Gene Set 0.00215 78 0.04436 20 Genes in module_297 www.broad.mit.e...
Broad module_107 View Gene Set 0.00227 77 0.04481 23 Genes in module_107 www.broad.mit.e...
Broad module_40 View Gene Set 0.002424 81 0.04586 24 Genes in module_40 www.broad.mit.e...

Gene Set Collection: Broad.c5.MF

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 OXIDOREDUCTASE_ACTIVITY View Gene Set 4.668e-06 280 0.001848 1 Genes annotated by the GO term GO:0016491. Catalysis of an oxidation-reduction (redox) reaction a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized while the other acts as hydrogen or electron acceptor and becomes reduced. www.broad.mit.e...
Broad OXIDOREDUCTASE_ACTIVITY_GO_0016616 View Gene Set 9.879e-05 57 0.01304 2 Genes annotated by the GO term GO:0016616. Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP. www.broad.mit.e...
Broad OXIDOREDUCTASE_ACTIVITY_ACTING_ON_CH_OH_GROUP_OF_DONORS View Gene Set 8.378e-05 63 0.01304 2 Genes annotated by the GO term GO:0016614. Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. 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 10830953 View Gene Set 5.279e-06 262 0.01324 1 The DNA sequence of human chromosome 21. www.ncbi.nlm.ni...
PMID 19027726 View Gene Set 2.402e-05 73 0.03011 2 The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. 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 chr17_15-20Mb View Gene Set 5.655e-06 50 0.0063 1 Genomic tile: chr17 ; 15000001-20000001 Mb genome.ucsc.edu...
Null chr14_20-25Mb View Gene Set 1.289e-05 56 0.007179 2 Genomic tile: chr14 ; 20000001-25000001 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 PS50404 View Gene Set 3.932e-05 25 0.0289 1 GST_NTER expasy.org/pros...
Null PS50405 View Gene Set 8.98e-05 38 0.033 2 GST_CTER expasy.org/pros...

Gene Set Collection: Enzyme

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 EC:1.14.13.8 View Gene Set 0.0004372 5 0.03454 1 Flavin-containing monooxygenase expasy.org/enzy...
Null EC:2.5.1.18 View Gene Set 0.0002593 20 0.03454 1 Glutathione transferase expasy.org/enzy...

Gene Set Collection: ppi.HPRD

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 ppi.MMP9 View Gene Set 1.86e-05 20 0.04416 1 Protein-protein-interaction for MMP9 www.ncbi.nlm.ni...

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 Interferon alpha/beta signaling View Gene Set 7.392e-08 65 8.257e-05 1 REACTOME - Interferon alpha/beta signaling gene set www.pathwaycomm...
Null Interferon Signaling View Gene Set 1.624e-07 86 9.072e-05 2 REACTOME - Interferon Signaling gene set www.pathwaycomm...
Null Interferon gamma signaling View Gene Set 9.412e-05 48 0.03505 3 REACTOME - Interferon gamma signaling 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-454 View Gene Set 0.0002575 769 0.0486 1 microRNA targets for hsa-miR-454 from mirbase.targets www.mirbase.org...
Null hsa-miR-518e* View Gene Set 0.0003417 584 0.0486 1 microRNA targets for hsa-miR-518e* from mirbase.targets www.mirbase.org...
Null hsa-miR-518f* View Gene Set 9.215e-05 582 0.0486 1 microRNA targets for hsa-miR-518f* from mirbase.targets www.mirbase.org...
Null hsa-miR-7-2* View Gene Set 0.0002106 531 0.0486 1 microRNA targets for hsa-miR-7-2* from mirbase.targets www.mirbase.org...
Null hsa-miR-875-3p View Gene Set 0.0002898 739 0.0486 1 microRNA targets for hsa-miR-875-3p from mirbase.targets www.mirbase.org...

Gene Set Collection: hprdBatch.DOWN

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 EGFR1 Signaling Pathway View Gene Set 0.0007968 98 0.01514 1 From NetPath for EGFR1 Signaling Pathway www.netpath.org...

Gene Set Collection: hprdManual.UP

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 TNFalpha View Gene Set 0.0006137 113 0.01473 1 From NetPath for TNFalpha www.netpath.org...