Results

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Go to: Gene Set Collection: KEGG
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Go to: Gene Set Collection: Broad.c4.CGN
Go to: Gene Set Collection: Broad.c4.CM
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Go to: Gene Set Collection: hprdManual.UP
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Go to: Gene Set Collection: hprdManual.DIFFERENT

AFA results for: VPA2e04.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 1.324e-08 1120 2.833e-06 1 Metabolic pathways www.genome.jp/d...
KEGG 00980 View Gene Set 3.392e-05 71 0.003629 2 Metabolism of xenobiotics by cytochrome P450 www.genome.jp/d...
KEGG 00982 View Gene Set 9.937e-05 73 0.005316 3 Drug metabolism - cytochrome P450 www.genome.jp/d...
KEGG 04142 View Gene Set 9.695e-05 121 0.005316 3 Lysosome www.genome.jp/d...
KEGG 04145 View Gene Set 0.0003487 158 0.01418 5 Phagosome www.genome.jp/d...
KEGG 04360 View Gene Set 0.0003976 129 0.01418 5 Axon guidance www.genome.jp/d...
KEGG 04146 View Gene Set 0.0005515 78 0.01686 7 Peroxisome www.genome.jp/d...
KEGG 00480 View Gene Set 0.0007664 50 0.0205 8 Glutathione metabolism www.genome.jp/d...
KEGG 00100 View Gene Set 0.0008678 17 0.02064 9 Steroid biosynthesis 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:0016020 View Gene Set 2.948e-15 7286 3.938e-11 1 membrane amigo.geneontol...
GO GO:0044444 View Gene Set 4.021e-12 5184 2.686e-08 2 cytoplasmic part amigo.geneontol...
GO GO:0044425 View Gene Set 1.23e-11 6145 5.478e-08 3 membrane part amigo.geneontol...
GO GO:0005737 View Gene Set 2.327e-09 7676 6.417e-06 4 cytoplasm amigo.geneontol...
GO GO:0016021 View Gene Set 2.877e-09 5278 6.417e-06 4 integral to membrane amigo.geneontol...
GO GO:0031224 View Gene Set 2.882e-09 5387 6.417e-06 4 intrinsic to membrane amigo.geneontol...
GO GO:0003824 View Gene Set 1.537e-08 5198 2.933e-05 7 catalytic activity amigo.geneontol...
GO GO:0030136 View Gene Set 6.787e-08 147 0.0001133 8 clathrin-coated vesicle amigo.geneontol...
GO GO:0005886 View Gene Set 7.764e-08 3759 0.0001152 9 plasma membrane amigo.geneontol...
GO GO:0005739 View Gene Set 2.41e-07 1274 0.000322 10 mitochondrion amigo.geneontol...
GO GO:0031090 View Gene Set 3.098e-07 1905 0.0003762 11 organelle membrane amigo.geneontol...
GO GO:0050662 View Gene Set 1.118e-06 176 0.001244 12 coenzyme binding amigo.geneontol...
GO GO:0006629 View Gene Set 1.698e-06 910 0.001512 13 lipid metabolic process amigo.geneontol...
GO GO:0016614 View Gene Set 1.629e-06 115 0.001512 13 oxidoreductase activity acting on CH-OH group of donors amigo.geneontol...
GO GO:0048037 View Gene Set 1.645e-06 249 0.001512 13 cofactor binding amigo.geneontol...
GO GO:0044459 View Gene Set 2.74e-06 2023 0.002288 16 plasma membrane part amigo.geneontol...
GO GO:0030135 View Gene Set 2.993e-06 179 0.002352 17 coated vesicle amigo.geneontol...
GO GO:0016616 View Gene Set 4.778e-06 104 0.003546 18 oxidoreductase activity acting on the CH-OH group of donors NAD or NADP as acceptor amigo.geneontol...
GO GO:0055114 View Gene Set 5.715e-06 647 0.004018 19 oxidation reduction amigo.geneontol...
GO GO:0016491 View Gene Set 1.171e-05 689 0.00782 20 oxidoreductase activity amigo.geneontol...
GO GO:0044281 View Gene Set 2e-05 1698 0.01246 21 small molecule metabolic process amigo.geneontol...
GO GO:0030665 View Gene Set 2.051e-05 79 0.01246 21 clathrin coated vesicle membrane amigo.geneontol...
GO GO:0012505 View Gene Set 2.26e-05 1454 0.01313 23 endomembrane system amigo.geneontol...
GO GO:0008202 View Gene Set 7.536e-05 238 0.04027 24 steroid metabolic process amigo.geneontol...
GO GO:0070011 View Gene Set 7.429e-05 552 0.04027 24 peptidase activity acting on L-amino acid peptides amigo.geneontol...
GO GO:0005773 View Gene Set 8.469e-05 286 0.0421 26 vacuole amigo.geneontol...
GO GO:0030659 View Gene Set 8.508e-05 235 0.0421 26 cytoplasmic vesicle membrane amigo.geneontol...
GO GO:0016023 View Gene Set 9.821e-05 651 0.04686 28 cytoplasmic membrane-bounded vesicle 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 chr14q11 View Gene Set 1.369e-05 289 0.004464 1 Genes in cytogenetic band chr14q11 www.broad.mit.e...
Broad chr17p11 View Gene Set 8.707e-05 118 0.01419 2 Genes in cytogenetic band chr17p11 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 1.26e-29 453 3.013e-26 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 1.478e-17 217 1.767e-14 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_LUMINAL_VS_MESENCHYMAL_UP View Gene Set 2.907e-14 422 2.318e-11 3 Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. www.broad.mit.e...
Broad CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 View Gene Set 1.274e-12 681 7.619e-10 4 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 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP View Gene Set 4.636e-10 114 2.218e-07 5 Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. www.broad.mit.e...
Broad MASSARWEH_TAMOXIFEN_RESISTANCE_UP View Gene Set 6.451e-10 531 2.572e-07 6 Genes up-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. www.broad.mit.e...
Broad BROWNE_INTERFERON_RESPONSIVE_GENES View Gene Set 4.039e-09 67 1.38e-06 7 Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. www.broad.mit.e...
Broad MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN View Gene Set 4.869e-09 317 1.456e-06 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 JISON_SICKLE_CELL_DISEASE_UP View Gene Set 1.389e-08 175 3.692e-06 9 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 STEIN_ESRRA_TARGETS_UP View Gene Set 1.819e-08 368 4.35e-06 10 Genes up-regulated by ESRRA [Gene ID=2101] only. www.broad.mit.e...
Broad DELYS_THYROID_CANCER_UP View Gene Set 2.563e-08 397 5.572e-06 11 Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. www.broad.mit.e...
Broad CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN View Gene Set 3.913e-08 437 7.799e-06 12 Genes down-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. www.broad.mit.e...
Broad TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP View Gene Set 5.941e-08 182 1.093e-05 13 Genes up-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [Gene ID=861 862] fusion. www.broad.mit.e...
Broad ROZANOV_MMP14_TARGETS_UP View Gene Set 1.219e-07 260 2.083e-05 14 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 BERENJENO_TRANSFORMED_BY_RHOA_DN View Gene Set 1.407e-07 353 2.244e-05 15 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 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP View Gene Set 1.7e-07 716 2.481e-05 16 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 MOSERLE_IFNA_RESPONSE View Gene Set 1.763e-07 30 2.481e-05 16 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 JAEGER_METASTASIS_DN View Gene Set 1.93e-07 252 2.565e-05 18 Genes down-regulated in metastases from malignant melanoma compared to the primary tumors. www.broad.mit.e...
Broad KOBAYASHI_EGFR_SIGNALING_24HR_UP View Gene Set 2.094e-07 96 2.636e-05 19 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 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP View Gene Set 2.242e-07 72 2.682e-05 20 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 WU_CELL_MIGRATION View Gene Set 2.55e-07 182 2.905e-05 21 Genes associated with migration rate of 40 human bladder cancer cells. www.broad.mit.e...
Broad AIGNER_ZEB1_TARGETS View Gene Set 2.969e-07 29 3.228e-05 22 Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [Gene ID=6935] by RNAi. www.broad.mit.e...
Broad HAN_SATB1_TARGETS_DN View Gene Set 3.785e-07 320 3.936e-05 23 Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [Gene ID=6304] by RNAi. www.broad.mit.e...
Broad RUIZ_TNC_TARGETS_UP View Gene Set 4.384e-07 145 4.369e-05 24 Genes up-regulated in T98G cells (glioblastoma) by TNC [Gene ID=3371]. www.broad.mit.e...
Broad LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP View Gene Set 6.475e-07 178 6.196e-05 25 Genes up-regulated in Wilm's tumor samples compared to fetal kidney. www.broad.mit.e...
Broad ONDER_CDH1_TARGETS_1_UP View Gene Set 7.296e-07 131 6.713e-05 26 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 FARMER_BREAST_CANCER_APOCRINE VS LUMINAL View Gene Set 9.809e-07 312 8.69e-05 27 Genes which best discriminate between two groups of breast cancer according to the status of ESR1 and AR [Gene ID=2099 367]: apocrine (ESR1- AR+) and luminal (ESR1+ AR+). www.broad.mit.e...
Broad BASAKI_YBX1_TARGETS_DN View Gene Set 1.028e-06 356 8.779e-05 28 Genes down-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [Gene ID=4904] knockdown by RNAi. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN View Gene Set 1.284e-06 155 0.0001059 29 Marker genes down-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. www.broad.mit.e...
Broad DODD_NASOPHARYNGEAL_CARCINOMA_UP View Gene Set 1.479e-06 1582 0.0001179 30 Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. www.broad.mit.e...
Broad KOBAYASHI_RESPONSE_TO_ROMIDEPSIN View Gene Set 1.632e-06 19 0.0001259 31 Genes up-regulated in MM-LH cells (malignant melanoma) after treatment with the HDAC inhibitor romidepsin (FK228) [PubChem=5352062]. www.broad.mit.e...
Broad BLALOCK_ALZHEIMERS_DISEASE_DN View Gene Set 1.896e-06 1209 0.0001417 32 Genes down-regulated in brain from patients with Alzheimer's disease. www.broad.mit.e...
Broad STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN View Gene Set 2.285e-06 437 0.0001657 33 Genes down-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS View Gene Set 2.508e-06 508 0.0001765 34 Genes regulated by ESRRA [Gene ID=2101] in MCF-7 cells (breast cancer). www.broad.mit.e...
Broad CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 View Gene Set 4.565e-06 446 0.000312 35 The 'group 5 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [Gene ID=2099 2064]. www.broad.mit.e...
Broad SANA_TNF_SIGNALING_UP View Gene Set 5.587e-06 75 0.0003712 36 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 NUYTTEN_EZH2_TARGETS_UP View Gene Set 7.873e-06 944 0.000509 37 Genes up-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [Gene ID=2146] by RNAi. www.broad.mit.e...
Broad CASTELLANO_NRAS_TARGETS_UP View Gene Set 8.705e-06 59 0.000548 38 Genes up-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [Gene ID=4893] knockout mice. www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP View Gene Set 9.174e-06 186 0.0005627 39 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 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN View Gene Set 9.669e-06 532 0.0005782 40 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 ONDER_CDH1_TARGETS_2_UP View Gene Set 1.146e-05 249 0.0006684 41 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 ELVIDGE_HYPOXIA_UP View Gene Set 1.21e-05 163 0.0006775 42 Genes up-regulated in MCF7 cells (breast cancer) under hypoxia conditions. www.broad.mit.e...
Broad BECKER_TAMOXIFEN_RESISTANCE_UP View Gene Set 1.218e-05 38 0.0006775 42 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 CHANG_CORE_SERUM_RESPONSE_DN View Gene Set 1.265e-05 30 0.0006876 44 Down-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. www.broad.mit.e...
Broad GOZGIT_ESR1_TARGETS_DN View Gene Set 1.522e-05 710 0.0008088 45 Genes down-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [Gene ID=2099]) compared to the parental MCF7 cells which do. www.broad.mit.e...
Broad HORIUCHI_WTAP_TARGETS_UP View Gene Set 1.595e-05 284 0.0008296 46 Genes up-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [Gene ID=9589] by RNAi. www.broad.mit.e...
Broad GALE_APL_WITH_FLT3_MUTATED_DN View Gene Set 2.842e-05 17 0.001418 47 Genes down-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [Gene ID=2322]. www.broad.mit.e...
Broad YAGI_AML_FAB_MARKERS View Gene Set 2.906e-05 189 0.001418 47 Genes specifically expressed in FAB subtypes M2 M4 M5 and M7 of pediatric AML (acute myeloid leukemia). www.broad.mit.e...
Broad REN_ALVEOLAR_RHABDOMYOSARCOMA_DN View Gene Set 2.866e-05 402 0.001418 47 Genes commonly down-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [Gene ID=5077 2308] fusion. www.broad.mit.e...
Broad KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP View Gene Set 2.966e-05 126 0.001419 50 Genes up-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. www.broad.mit.e...
Broad LINDSTEDT_DENDRITIC_CELL_MATURATION_A View Gene Set 3.64e-05 54 0.001707 51 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 MULLIGHAN_MLL_SIGNATURE_1_UP View Gene Set 4.122e-05 358 0.001896 52 The 'MLL signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [Gene ID=4297] compared to all AML cases with the intact gene. www.broad.mit.e...
Broad ONKEN_UVEAL_MELANOMA_DN View Gene Set 5.106e-05 509 0.002283 53 Genes down-regulated in uveal melanoma: class 2 vs class 1 tumors. www.broad.mit.e...
Broad TSAI_DNAJB4_TARGETS_UP View Gene Set 5.155e-05 13 0.002283 53 Genes up-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [Gene ID=11080] off a plasmid vector. www.broad.mit.e...
Broad BRUECKNER_TARGETS_OF_MIRLET7A3_UP View Gene Set 5.339e-05 105 0.002322 55 Genes up-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [Gene ID=406883] microRNA off a plasmid vector. www.broad.mit.e...
Broad SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN View Gene Set 6.462e-05 571 0.002719 56 Genes down-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. www.broad.mit.e...
Broad ONDER_CDH1_SIGNALING_VIA_CTNNB1 View Gene Set 6.479e-05 81 0.002719 56 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 RODRIGUES_DCC_TARGETS_DN View Gene Set 7.563e-05 121 0.003063 58 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 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP View Gene Set 7.474e-05 174 0.003063 58 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 LANDIS_ERBB2_BREAST_TUMORS_324_UP View Gene Set 7.683e-05 132 0.003063 58 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 CHANG_IMMORTALIZED_BY_HPV31_DN View Gene Set 8.738e-05 47 0.003426 61 Genes down-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. www.broad.mit.e...
Broad PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP View Gene Set 9.077e-05 257 0.003502 62 Genes up-regulated in post-GC BCL6 [Gene ID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [Gene ID=4609] driven pre-GC lymphoma; GC = germinal center. www.broad.mit.e...
Broad TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP View Gene Set 9.927e-05 153 0.003695 63 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 SMID_BREAST_CANCER_ERBB2_UP View Gene Set 0.0001004 138 0.003695 63 Genes up-regulated in the erbb2 subype of breast cancer samples characterized by higher expression of ERBB2 [Gene ID=2064]. www.broad.mit.e...
Broad WANG_CISPLATIN_RESPONSE_AND_XPC_UP View Gene Set 9.913e-05 135 0.003695 63 Genes up-regulated in fibroblasts with defective XPC [Gene ID=7508] in response to cisplatin [PubChem=2767]. www.broad.mit.e...
Broad HUANG_FOXA2_TARGETS_DN View Gene Set 0.0001092 36 0.003957 66 Genes down-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. www.broad.mit.e...
Broad LANDIS_BREAST_CANCER_PROGRESSION_UP View Gene Set 0.0001136 42 0.004057 67 Genes up-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. www.broad.mit.e...
Broad ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP View Gene Set 0.0001172 208 0.004124 68 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 ROSS_AML_OF_FAB_M7_TYPE View Gene Set 0.0001205 67 0.004179 69 Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype FAB M7 (also known as acute megakaryoblastic leukemia AMKL). www.broad.mit.e...
Broad BROWNE_HCMV_INFECTION_30MIN_UP View Gene Set 0.0001363 53 0.004656 70 Genes up-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). www.broad.mit.e...
Broad SEKI_INFLAMMATORY_RESPONSE_LPS_UP View Gene Set 0.0001465 75 0.004935 71 Genes up-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). www.broad.mit.e...
Broad WIELAND_UP_BY_HBV_INFECTION View Gene Set 0.0001495 98 0.004967 72 Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. www.broad.mit.e...
Broad ZHANG_INTERFERON_RESPONSE View Gene Set 0.0001578 21 0.005171 73 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 HOLLMAN_APOPTOSIS_VIA_CD40_DN View Gene Set 0.0001607 255 0.005194 74 Genes down-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [Gene ID=958] relative to the resistant ones. www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP View Gene Set 0.0001998 101 0.006373 75 Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. www.broad.mit.e...
Broad RIGGINS_TAMOXIFEN_RESISTANCE_DN View Gene Set 0.000209 211 0.006577 76 Genes down-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. www.broad.mit.e...
Broad CAIRO_LIVER_DEVELOPMENT_DN View Gene Set 0.0002143 208 0.006657 77 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 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN View Gene Set 0.0002353 104 0.007216 78 Genes down-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). www.broad.mit.e...
Broad FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN View Gene Set 0.0002409 431 0.007294 79 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 BAELDE_DIABETIC_NEPHROPATHY_DN View Gene Set 0.0003019 35 0.009028 80 Top 50 down-regulated genes in glomeruli from kidneys with diabetic nephropathy (type 2 diabetes mellitus). www.broad.mit.e...
Broad JI_METASTASIS_REPRESSED_BY_STK11 View Gene Set 0.0003171 23 0.009092 81 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...
Broad SANA_RESPONSE_TO_IFNG_UP View Gene Set 0.0003121 68 0.009092 81 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 SMID_BREAST_CANCER_BASAL_DN View Gene Set 0.0003182 664 0.009092 81 Genes down-regulated in basal subtype of breast cancer samles. www.broad.mit.e...
Broad GAJATE_RESPONSE_TO_TRABECTEDIN_UP View Gene Set 0.0003193 53 0.009092 81 Genes up-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. www.broad.mit.e...
Broad LIU_PROSTATE_CANCER_DN View Gene Set 0.0003315 446 0.009147 85 Genes down-regulated in prostate cancer samples. www.broad.mit.e...
Broad BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX View Gene Set 0.0003327 10 0.009147 85 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 MOOTHA_HUMAN_MITODB_6_2002 View Gene Set 0.0003255 420 0.009147 85 Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. www.broad.mit.e...
Broad SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN View Gene Set 0.0003472 296 0.009438 88 Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. www.broad.mit.e...
Broad CHEBOTAEV_GR_TARGETS_UP View Gene Set 0.0003566 69 0.009466 89 Genes up-regulated in follicular epithelial stem cells after transgenic expression of GR [Gene ID=2908] under control of the keratin5 (K5) [Gene ID=3852] promoter. www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP View Gene Set 0.0003549 869 0.009466 89 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 WANG_SMARCE1_TARGETS_UP View Gene Set 0.0003601 158 0.009466 89 Genes up-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [Gene ID=6605] off a retroviral vector. www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_BY_DMOG_UP View Gene Set 0.0003856 125 0.01003 92 Genes up-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. www.broad.mit.e...
Broad NEWMAN_ERCC6_TARGETS_UP View Gene Set 0.0003918 25 0.01008 93 Genes up-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [Gene ID=2074] off a plasmid vector. www.broad.mit.e...
Broad KIM_MYCN_AMPLIFICATION_TARGETS_DN View Gene Set 0.0004508 78 0.01147 94 Genes negatively correlated with amplifications of MYCN [Gene ID=4613] in the SCLC (small cell lung cancer) cell lines. www.broad.mit.e...
Broad BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP View Gene Set 0.0004572 61 0.01151 95 Up-regulated genes in hepatocellular carcinoma (HCC) subclass G6 defined by unsupervised clustering. www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 View Gene Set 0.0004782 68 0.01191 96 Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 9. www.broad.mit.e...
Broad KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP View Gene Set 0.000497 126 0.01213 97 Genes up-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. www.broad.mit.e...
Broad LINDGREN_BLADDER_CANCER_CLUSTER_1_UP View Gene Set 0.0004967 109 0.01213 97 Genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. www.broad.mit.e...
Broad HINATA_NFKB_TARGETS_KERATINOCYTE_UP View Gene Set 0.0005071 71 0.01225 99 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 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP View Gene Set 0.0005157 14 0.01233 100 Genes up-regulated synergistically in NB4 cells (acute promyelocytic leukemia APL) by tretinoin and NSC682994 [PubChem=5538 388304]. www.broad.mit.e...
Broad HOOI_ST7_TARGETS_DN View Gene Set 0.000532 108 0.0126 101 Genes down-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [Gene ID=7982] off a plasmid vector. www.broad.mit.e...
Broad MARKEY_RB1_ACUTE_LOF_UP View Gene Set 0.0005581 202 0.01309 102 Genes up-regulated in adult fibroblasts with inactivated RB1 [Gene ID=5925] by Cre-lox: acute loss of function (LOF) of RB1. www.broad.mit.e...
Broad SMID_BREAST_CANCER_LUMINAL_B_DN View Gene Set 0.0005846 549 0.01358 103 Genes down-regulated in the luminal B subtype of breast cancer. www.broad.mit.e...
Broad OSAWA_TNF_TARGETS View Gene Set 0.0006124 10 0.01409 104 Genes up-regulated in Hc cells (normal hepatocyte) by TNF [Gene ID=7124]. www.broad.mit.e...
Broad DAUER_STAT3_TARGETS_DN View Gene Set 0.0006226 37 0.01418 105 Top 50 genes down-regulated in A549 cells (lung cancer) expressing STAT3 [Gene ID=6774] off an adenovirus vector. www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON View Gene Set 0.000664 128 0.01484 106 Genes within amplicon 8q12-q22 identified in a copy number alterations study of 191 breast tumor samples. www.broad.mit.e...
Broad SMITH_LIVER_CANCER View Gene Set 0.0006582 31 0.01484 106 Potential marker genes specifically up-regulated in the majority of hepatocellular carcinoma (HCC) tumors. www.broad.mit.e...
Broad BOWIE_RESPONSE_TO_TAMOXIFEN View Gene Set 0.0006736 14 0.01492 108 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 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP View Gene Set 0.0007714 394 0.01693 109 Genes up-regulated in peripheral blood mononucleocytes by HGF [Gene ID=3082] compared to those regulated by CSF2RB (GM-CSF) [Gene ID=1437] and IL4 [Gene ID=3565]. www.broad.mit.e...
Broad HOSHIDA_LIVER_CANCER_SUBCLASS_S3 View Gene Set 0.0008383 266 0.01823 110 Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. www.broad.mit.e...
Broad CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN View Gene Set 0.0008917 144 0.01922 111 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 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP View Gene Set 0.0009542 78 0.02038 112 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 ROSS_AML_WITH_MLL_FUSIONS View Gene Set 0.0009856 76 0.02086 113 Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtypes with chimeric MLL fusions [Gene ID=4297]. www.broad.mit.e...
Broad NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN View Gene Set 0.001079 583 0.02245 114 Down-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. www.broad.mit.e...
Broad MISSIAGLIA_REGULATED_BY_METHYLATION_UP View Gene Set 0.001078 99 0.02245 114 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 UROSEVIC_RESPONSE_TO_IMIQUIMOD View Gene Set 0.001109 16 0.02287 116 Interferon cluster genes up-regulated in skin tumors treated with imiquimod [PubChem=57469]. www.broad.mit.e...
Broad LEE_EARLY_T_LYMPHOCYTE_DN View Gene Set 0.001139 44 0.02328 117 Genes down-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. www.broad.mit.e...
Broad HUANG_DASATINIB_RESISTANCE_UP View Gene Set 0.00115 75 0.02331 118 Genes whose expression positively correlated with sensitivity of breast cancer cell lines to dasatinib [PubChem=3062316]. www.broad.mit.e...
Broad ROETH_TERT_TARGETS_UP View Gene Set 0.001203 8 0.02408 119 Genes up-regulated in T lymphocytes overexpressing TERT [Gene ID=7015] off a retrovirus vector. www.broad.mit.e...
Broad BOYLAN_MULTIPLE_MYELOMA_C_D_DN View Gene Set 0.001208 232 0.02408 119 Genes down-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [Gene ID=598 4609] in plasma cells. www.broad.mit.e...
Broad DER_IFN_ALPHA_RESPONSE_UP View Gene Set 0.001225 57 0.02422 121 Genes up-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. www.broad.mit.e...
Broad LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL View Gene Set 0.001267 15 0.02484 122 Genes changed in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of reciprocal congenic strains D.B. Chr3 (DB) B.D. Chr3 (BD) and the parental strains B6 and D2. www.broad.mit.e...
Broad LEI_MYB_TARGETS View Gene Set 0.001296 13 0.0252 123 Myb-regulated genes in MCF7 (breast cancer) and lung epithelial cell lines overexpressing MYBL2 MYBL1 or MYB [Gene ID=4605 4603 4602]. www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0 View Gene Set 0.001308 69 0.02524 124 Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 0. www.broad.mit.e...
Broad MOHANKUMAR_TLX1_TARGETS_DN View Gene Set 0.001353 158 0.0259 125 Down-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [Gene ID=3195]. www.broad.mit.e...
Broad ABE_VEGFA_TARGETS_2HR View Gene Set 0.001452 20 0.02756 126 Genes up-regulated in HUVEC cells (endothelium) at 2 h after VEGFA [Gene ID=7422] stimulation. www.broad.mit.e...
Broad WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP View Gene Set 0.001592 131 0.02999 127 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 IVANOVA_HEMATOPOIESIS_MATURE_CELL View Gene Set 0.001676 96 0.03132 128 Genes in the expression cluster 'MBC Shared': up-regulated in mature blood cell populations from adult bone marrow and fetal liver. www.broad.mit.e...
Broad ALCALA_APOPTOSIS View Gene Set 0.001789 87 0.03317 129 Genes able to induce cell death in an expression cDNA library screen. www.broad.mit.e...
Broad MULLIGHAN_MLL_SIGNATURE_2_UP View Gene Set 0.001855 393 0.0339 130 The 'MLL signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [Gene ID=4297] compared to the AML cases with intact MLL and NPM1 [Gene ID=4869]. www.broad.mit.e...
Broad HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN View Gene Set 0.001857 70 0.0339 130 Genes down-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [Gene ID=3205 4211]. www.broad.mit.e...
Broad PARENT_MTOR_SIGNALING_UP View Gene Set 0.001906 541 0.03408 132 Genes up-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [Gene ID=2475]. www.broad.mit.e...
Broad THUM_SYSTOLIC_HEART_FAILURE_UP View Gene Set 0.001888 393 0.03408 132 Genes up-regulated in samples with systolic heart failure compared to normal hearts. www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP View Gene Set 0.001909 399 0.03408 132 Genes up-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. www.broad.mit.e...
Broad ALONSO_METASTASIS_UP View Gene Set 0.001931 152 0.03422 135 Up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. www.broad.mit.e...
Broad SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN View Gene Set 0.001959 306 0.03445 136 Genes down-regulated in bone relapse of breast cancer. www.broad.mit.e...
Broad MARKS_HDAC_TARGETS_UP View Gene Set 0.001997 21 0.03487 137 Genes whose transcription is altered by histone deacetylase inhibitors. www.broad.mit.e...
Broad BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS View Gene Set 0.00204 23 0.03515 138 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 VANTVEER_BREAST_CANCER_ESR1_UP View Gene Set 0.002046 140 0.03515 138 Up-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [Gene ID=2099] expression: ER(+) vs ER(-) tumors. www.broad.mit.e...
Broad COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN View Gene Set 0.002057 118 0.03515 138 'Early-TGFB1 signature': genes overexpressed in primary hepatocytes at an early phase of TGFB1 [Gene ID=7040] treatment; is associated with a less invasive phenotype. www.broad.mit.e...
Broad NAGASHIMA_NRG1_SIGNALING_DN View Gene Set 0.002162 53 0.03641 141 Genes down-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [Gene ID=3084]. www.broad.mit.e...
Broad ENK_UV_RESPONSE_KERATINOCYTE_UP View Gene Set 0.002176 517 0.03641 141 Genes up-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. www.broad.mit.e...
Broad BROWNE_HCMV_INFECTION_48HR_UP View Gene Set 0.002163 175 0.03641 141 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 KRASNOSELSKAYA_ILF3_TARGETS_UP View Gene Set 0.002256 31 0.03748 144 Up-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [Gene ID=3609]. www.broad.mit.e...
Broad PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN View Gene Set 0.002332 140 0.0382 145 Genes down-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. www.broad.mit.e...
Broad ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP View Gene Set 0.002324 31 0.0382 145 The v1LDG set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. www.broad.mit.e...
Broad LE_EGR2_TARGETS_DN View Gene Set 0.002388 100 0.03885 147 Genes down-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [Gene ID=1959]. www.broad.mit.e...
Broad LU_AGING_BRAIN_DN View Gene Set 0.002411 255 0.03897 148 Genes down-regulated in postmortem brain frontal cortex samples from old subjects compared to those from the young ones. www.broad.mit.e...
Broad ENK_UV_RESPONSE_EPIDERMIS_UP View Gene Set 0.002451 283 0.03934 149 Genes up-regulated in epidermis after to UVB irradiation. www.broad.mit.e...
Broad NUYTTEN_NIPP1_TARGETS_UP View Gene Set 0.002558 657 0.04079 150 Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [Gene ID=5511] by RNAi. www.broad.mit.e...
Broad HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN View Gene Set 0.002628 55 0.04163 151 Genes down-regulated during differentiation from pre-BI to large pre-BII lymphocyte. www.broad.mit.e...
Broad HSIAO_LIVER_SPECIFIC_GENES View Gene Set 0.00275 236 0.04328 152 Liver selective genes www.broad.mit.e...
Broad DACOSTA_UV_RESPONSE_VIA_ERCC3_UP View Gene Set 0.002808 301 0.04391 153 Genes up-regulated in fibroblasts expressing mutant forms of ERCC3 [Gene ID=2071] after UV irradiation. www.broad.mit.e...
Broad YANG_BREAST_CANCER_ESR1_BULK_UP View Gene Set 0.002915 17 0.04472 154 Genes up-regulated in bulk samples from early primary breast tumors expressing ESR1 [Gene ID=2099] vs the ESR1 negative samples. www.broad.mit.e...
Broad SHEPARD_BMYB_MORPHOLINO_DN View Gene Set 0.002916 156 0.04472 154 Human orthologs of genes down-regulated in zebra fish after knockdown of BMYB [Gene ID=4605] by morpholino. www.broad.mit.e...
Broad SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 View Gene Set 0.002884 407 0.04472 154 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 BOYLAN_MULTIPLE_MYELOMA_PCA1_UP View Gene Set 0.002977 80 0.04535 157 Top up-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [Gene ID=598 4609]. www.broad.mit.e...
Broad PEREZ_TP63_TARGETS View Gene Set 0.003003 328 0.04544 158 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 MELLMAN_TUT1_TARGETS_DN View Gene Set 0.003021 47 0.04544 158 Genes down-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [Gene ID=64852] by RNAi. www.broad.mit.e...
Broad GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP View Gene Set 0.003043 28 0.04549 160 Genes up-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [Gene ID=6223]. www.broad.mit.e...
Broad LANDIS_ERBB2_BREAST_TUMORS_324_DN View Gene Set 0.003112 137 0.04606 161 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 KAAB_HEART_ATRIUM_VS_VENTRICLE_DN View Gene Set 0.00312 257 0.04606 161 Genes up-regulated in the ventricles of healthy hearts compared to atria. www.broad.mit.e...
Broad FRASOR_TAMOXIFEN_RESPONSE_UP View Gene Set 0.003147 46 0.04618 163 Genes preferentially up-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757 3478439]. www.broad.mit.e...
Broad MOOTHA_MITOCHONDRIA View Gene Set 0.003194 433 0.04658 164 Mitochondrial genes www.broad.mit.e...
Broad SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN View Gene Set 0.003248 83 0.0468 165 Genes down-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS non-invasive). www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13 View Gene Set 0.00324 158 0.0468 165 Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 13. www.broad.mit.e...
Broad RUTELLA_RESPONSE_TO_HGF_UP View Gene Set 0.003361 409 0.04815 167 Genes up-regulated in peripheral blood monocytes by HGF [Gene ID=3082]. www.broad.mit.e...
Broad EINAV_INTERFERON_SIGNATURE_IN_CANCER View Gene Set 0.003439 27 0.04897 168 A gene expression signature found in a subset of cancer patients suggestive of a deregulated immune or inflammatory response. www.broad.mit.e...
Broad GOZGIT_ESR1_TARGETS_UP View Gene Set 0.003471 141 0.04913 169 Genes up-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [Gene ID=2099]) compared to the parental MCF7 cells which do. 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_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 View Gene Set 3.392e-05 70 0.006161 1 Metabolism of xenobiotics by cytochrome P450 www.broad.mit.e...
Broad KEGG_DRUG_METABOLISM_CYTOCHROME_P450 View Gene Set 9.937e-05 72 0.006161 1 Drug metabolism - cytochrome P450 www.broad.mit.e...
Broad KEGG_LYSOSOME View Gene Set 9.695e-05 122 0.006161 1 Lysosome www.broad.mit.e...
Broad KEGG_AXON_GUIDANCE View Gene Set 0.0003976 129 0.01849 4 Axon guidance www.broad.mit.e...
Broad KEGG_PEROXISOME View Gene Set 0.0005515 78 0.02051 5 Peroxisome www.broad.mit.e...
Broad KEGG_STEROID_BIOSYNTHESIS View Gene Set 0.0008678 17 0.02306 6 Steroid biosynthesis www.broad.mit.e...
Broad KEGG_GLUTATHIONE_METABOLISM View Gene Set 0.0007664 50 0.02306 6 Glutathione metabolism 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_LYN View Gene Set 0.0001046 26 0.02327 1 Neighborhood of LYN www.broad.mit.e...
Broad GNF2_SERPINB5 View Gene Set 0.000109 25 0.02327 1 Neighborhood of SERPINB5 www.broad.mit.e...
Broad CAR_WBSCR22 View Gene Set 0.0002153 35 0.02898 3 Neighborhood of WBSCR22 www.broad.mit.e...
Broad GNF2_CDH3 View Gene Set 0.0002714 24 0.02898 3 Neighborhood of CDH3 www.broad.mit.e...
Broad CAR_MLANA View Gene Set 0.0004756 42 0.04061 5 Neighborhood of MLANA 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_180 View Gene Set 8.089e-08 113 3.672e-05 1 Genes in module_180 www.broad.mit.e...
Broad module_93 View Gene Set 2.978e-07 180 6.761e-05 2 Genes in module_93 www.broad.mit.e...
Broad module_6 View Gene Set 1.954e-06 403 0.0002956 3 Genes in module_6 www.broad.mit.e...
Broad module_5 View Gene Set 4.546e-06 420 0.000344 4 Genes in module_5 www.broad.mit.e...
Broad module_44 View Gene Set 3.8e-06 319 0.000344 4 Genes in module_44 www.broad.mit.e...
Broad module_342 View Gene Set 3.533e-06 195 0.000344 4 Genes in module_342 www.broad.mit.e...
Broad module_11 View Gene Set 2.039e-05 520 0.001323 7 Genes in module_11 www.broad.mit.e...
Broad module_45 View Gene Set 4.071e-05 563 0.002054 8 Genes in module_45 www.broad.mit.e...
Broad module_432 View Gene Set 3.747e-05 15 0.002054 8 Genes in module_432 www.broad.mit.e...
Broad module_139 View Gene Set 5.237e-05 74 0.002161 10 Genes in module_139 www.broad.mit.e...
Broad module_568 View Gene Set 4.905e-05 70 0.002161 10 Genes in module_568 www.broad.mit.e...
Broad module_12 View Gene Set 8.417e-05 346 0.002736 12 Genes in module_12 www.broad.mit.e...
Broad module_135 View Gene Set 8.51e-05 25 0.002736 12 Genes in module_135 www.broad.mit.e...
Broad module_357 View Gene Set 9.04e-05 78 0.002736 12 Genes in module_357 www.broad.mit.e...
Broad module_491 View Gene Set 8.43e-05 74 0.002736 12 Genes in module_491 www.broad.mit.e...
Broad module_23 View Gene Set 0.0001289 552 0.003632 16 Genes in module_23 www.broad.mit.e...
Broad module_137 View Gene Set 0.000136 525 0.003632 16 Genes in module_137 www.broad.mit.e...
Broad module_84 View Gene Set 0.0001461 526 0.003686 18 Genes in module_84 www.broad.mit.e...
Broad module_66 View Gene Set 0.0001807 530 0.004317 19 Genes in module_66 www.broad.mit.e...
Broad module_2 View Gene Set 0.000221 373 0.004665 20 Genes in module_2 www.broad.mit.e...
Broad module_88 View Gene Set 0.0002336 812 0.004665 20 Genes in module_88 www.broad.mit.e...
Broad module_100 View Gene Set 0.0002363 523 0.004665 20 Genes in module_100 www.broad.mit.e...
Broad module_151 View Gene Set 0.0002166 297 0.004665 20 Genes in module_151 www.broad.mit.e...
Broad module_55 View Gene Set 0.0002938 807 0.005133 24 Genes in module_55 www.broad.mit.e...
Broad module_101 View Gene Set 0.0003053 10 0.005133 24 Genes in module_101 www.broad.mit.e...
Broad module_249 View Gene Set 0.000303 21 0.005133 24 Genes in module_249 www.broad.mit.e...
Broad module_297 View Gene Set 0.0003043 78 0.005133 24 Genes in module_297 www.broad.mit.e...
Broad module_132 View Gene Set 0.0003176 13 0.005149 28 Genes in module_132 www.broad.mit.e...
Broad module_286 View Gene Set 0.000398 37 0.006231 29 Genes in module_286 www.broad.mit.e...
Broad module_154 View Gene Set 0.0005601 73 0.008476 30 Genes in module_154 www.broad.mit.e...
Broad module_24 View Gene Set 0.0006413 443 0.009098 31 Genes in module_24 www.broad.mit.e...
Broad module_114 View Gene Set 0.000624 314 0.009098 31 Genes in module_114 www.broad.mit.e...
Broad module_310 View Gene Set 0.0006779 21 0.009326 33 Genes in module_310 www.broad.mit.e...
Broad module_389 View Gene Set 0.000704 182 0.009401 34 Genes in module_389 www.broad.mit.e...
Broad module_87 View Gene Set 0.0008625 44 0.01119 35 Genes in module_87 www.broad.mit.e...
Broad module_212 View Gene Set 0.0009825 316 0.01239 36 Genes in module_212 www.broad.mit.e...
Broad module_92 View Gene Set 0.001164 146 0.01428 37 Genes in module_92 www.broad.mit.e...
Broad module_431 View Gene Set 0.001314 15 0.0157 38 Genes in module_431 www.broad.mit.e...
Broad module_26 View Gene Set 0.001629 178 0.01896 39 Genes in module_26 www.broad.mit.e...
Broad module_119 View Gene Set 0.002037 135 0.02283 40 Genes in module_119 www.broad.mit.e...
Broad module_207 View Gene Set 0.002062 195 0.02283 40 Genes in module_207 www.broad.mit.e...
Broad module_488 View Gene Set 0.002121 28 0.02292 42 Genes in module_488 www.broad.mit.e...
Broad module_86 View Gene Set 0.002238 43 0.02363 43 Genes in module_86 www.broad.mit.e...
Broad module_40 View Gene Set 0.002676 81 0.02761 44 Genes in module_40 www.broad.mit.e...
Broad module_144 View Gene Set 0.0029 8 0.02926 45 Genes in module_144 www.broad.mit.e...
Broad module_152 View Gene Set 0.00453 121 0.0447 46 Genes in module_152 www.broad.mit.e...
Broad module_107 View Gene Set 0.004768 77 0.04606 47 Genes in module_107 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 PEROXISOMAL_PART View Gene Set 0.0004045 13 0.02021 1 Genes annotated by the GO term GO:0044439. Any constituent part of a peroxisome 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...
Broad MICROBODY_PART View Gene Set 0.0004045 13 0.02021 1 Genes annotated by the GO term GO:0044438. Any constituent part of a microbody a cytoplasmic organelle spherical or oval in shape that is bounded by a single membrane and contains oxidative enzymes especially those utilizing hydrogen peroxide (H2O2). www.broad.mit.e...
Broad MICROBODY View Gene Set 0.0002813 46 0.02021 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 PLASMA_MEMBRANE_PART View Gene Set 0.0004338 1142 0.02021 1 Genes annotated by the GO term GO:0044459. Any constituent part of the plasma membrane the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. www.broad.mit.e...
Broad PEROXISOME View Gene Set 0.0002813 46 0.02021 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...
Broad INTRINSIC_TO_PLASMA_MEMBRANE View Gene Set 0.001465 978 0.03177 6 Genes annotated by the GO term GO:0031226. Located in the plasma membrane such that some covalently attached portion of the gene product for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor spans or is embedded in one or both leaflets of the membrane. www.broad.mit.e...
Broad PEROXISOMAL_MEMBRANE View Gene Set 0.00139 12 0.03177 6 Genes annotated by the GO term GO:0005778. The lipid bilayer surrounding a peroxisome. www.broad.mit.e...
Broad CYTOPLASMIC_PART View Gene Set 0.0009264 1350 0.03177 6 Genes annotated by the GO term GO:0044444. Any constituent part of the cytoplasm all of the contents of a cell excluding the plasma membrane and nucleus but including other subcellular structures. www.broad.mit.e...
Broad MEMBRANE_PART View Gene Set 0.0015 1632 0.03177 6 Genes annotated by the GO term GO:0044425. Any constituent part of a membrane a double layer of lipid molecules that encloses all cells and in eukaryotes many organelles; may be a single or double lipid bilayer; also includes associated proteins. www.broad.mit.e...
Broad MICROBODY_MEMBRANE View Gene Set 0.00139 12 0.03177 6 Genes annotated by the GO term GO:0031903. The lipid bilayer surrounding a microbody. www.broad.mit.e...
Broad INTEGRAL_TO_PLASMA_MEMBRANE View Gene Set 0.001334 964 0.03177 6 Genes annotated by the GO term GO:0005887. Penetrating at least one phospholipid bilayer of a plasma membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. www.broad.mit.e...
Broad MEMBRANE View Gene Set 0.002049 1939 0.03454 12 Genes annotated by the GO term GO:0016020. Double layer of lipid molecules that encloses all cells and in eukaryotes many organelles; may be a single or double lipid bilayer; also includes associated proteins. www.broad.mit.e...
Broad APICAL_JUNCTION_COMPLEX View Gene Set 0.002075 34 0.03454 12 Genes annotated by the GO term GO:0043296. A functional unit located near the cell apex at the points of contact between epithelial cells which in vertebrates is composed of the tight junction the zonula adherens and desmosomes and in invertebrates is composed of the subapical complex (SAC) the zonula adherens and the septate junction. Functions in the regulation of cell polarity tissue integrity and intercellular adhesion and permeability. www.broad.mit.e...
Broad APICOLATERAL_PLASMA_MEMBRANE View Gene Set 0.002075 34 0.03454 12 Genes annotated by the GO term GO:0016327. The apical end of the lateral plasma membrane of epithelial cells. www.broad.mit.e...
Broad CYTOPLASM View Gene Set 0.002746 2054 0.04266 15 Genes annotated by the GO term GO:0005737. All of the contents of a cell excluding the plasma membrane and nucleus but including other subcellular structures. www.broad.mit.e...
Broad INTRINSIC_TO_MEMBRANE View Gene Set 0.003766 1319 0.04876 16 Genes annotated by the GO term GO:0031224. Located in a membrane such that some covalently attached portion of the gene product for example part of a peptide sequence or some other covalently attached moiety such as a GPI anchor spans or is embedded in one or both leaflets of the membrane. www.broad.mit.e...
Broad LIPID_RAFT View Gene Set 0.003767 28 0.04876 16 Genes annotated by the GO term GO:0045121. Specialized membrane domains composed mainly of cholesterol and sphingolipids and relatively poor in polyunsaturated lipids such as glycerophospholipids. The formation of these membrane domains is promoted by the presence of cholesterol in the lipid bilayer: the rigid hexagonal rings of cholesterol can pack tightly against the saturated hydrocarbon chains of some membrane lipids allowing these lipids to assemble into cohesive units floating in the mass of loosely packed polyunsaturated plasma membrane components. www.broad.mit.e...
Broad PLASMA_MEMBRANE View Gene Set 0.003699 1392 0.04876 16 Genes annotated by the GO term GO:0005886. The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. www.broad.mit.e...
Broad INTEGRAL_TO_MEMBRANE View Gene Set 0.004064 1301 0.04984 19 Genes annotated by the GO term GO:0016021. Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein indicates that all or part of the peptide sequence is embedded in the membrane. 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_GO_0016616 View Gene Set 6.505e-07 57 0.0001288 1 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 4.039e-07 63 0.0001288 1 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...
Broad OXIDOREDUCTASE_ACTIVITY View Gene Set 1.396e-06 280 0.0001843 3 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 RECEPTOR_ACTIVITY View Gene Set 0.0003385 572 0.02681 4 Genes annotated by the GO term GO:0004872. Combining with an extracellular or intracellular messenger to initiate a change in cell activity. www.broad.mit.e...
Broad GLUTATHIONE_TRANSFERASE_ACTIVITY View Gene Set 0.0003249 15 0.02681 4 Genes annotated by the GO term GO:0004364. Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic aromatic or heterocyclic group; X may be a sulfate nitrile or halide group. www.broad.mit.e...

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 chr14_20-25Mb View Gene Set 1.505e-05 56 0.01676 1 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 2.192e-05 25 0.01611 1 GST_NTER expasy.org/pros...
Null PS50003 View Gene Set 6.613e-05 259 0.0243 2 PH_DOMAIN expasy.org/pros...
Null PS50405 View Gene Set 0.0001005 38 0.02462 3 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:2.5.1.18 View Gene Set 7.965e-05 20 0.01258 1 Glutathione transferase expasy.org/enzy...
Null EC:2.7.10.2 View Gene Set 0.0008862 24 0.04868 2 Non-specific protein-tyrosine kinase expasy.org/enzy...
Null EC:3.6.3.14 View Gene Set 0.0009244 45 0.04868 2 H(+)-transporting two-sector ATPase expasy.org/enzy...

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 glutathione-mediated detoxification View Gene Set 4.017e-05 19 0.01044 1 HUMANCYC - glutathione-mediated detoxification gene set www.pathwaycomm...
Null superpathway of cholesterol biosynthesis View Gene Set 0.000258 25 0.03354 2 HUMANCYC - superpathway of cholesterol biosynthesis 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-124 View Gene Set 2.617e-07 793 0.0001861 1 microRNA targets for hsa-miR-124 from mirbase.targets www.mirbase.org...
Null hsa-miR-871 View Gene Set 1.265e-05 707 0.004498 2 microRNA targets for hsa-miR-871 from mirbase.targets www.mirbase.org...
Null hsa-miR-19a* View Gene Set 4.714e-05 536 0.01117 3 microRNA targets for hsa-miR-19a* from mirbase.targets www.mirbase.org...
Null hsa-miR-455-5p View Gene Set 0.0001177 739 0.02093 4 microRNA targets for hsa-miR-455-5p from mirbase.targets www.mirbase.org...
Null hsa-miR-330-3p View Gene Set 0.0003499 765 0.04594 5 microRNA targets for hsa-miR-330-3p from mirbase.targets www.mirbase.org...
Null hsa-miR-340 View Gene Set 0.0003877 581 0.04594 5 microRNA targets for hsa-miR-340 from mirbase.targets www.mirbase.org...

Gene Set Collection: miRNAtargetUnion

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 mirbase.mirtarget2.tarbase.targetsUnion.hsa-miR-124 View Gene Set 1.685e-05 1174 0.03899 1 microRNA targets for mirbase.mirtarget2.tarbase.targetsUnion.hsa-miR-124 from miRNAtargetUnion 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 6.611e-05 98 0.001256 1 From NetPath for EGFR1 Signaling Pathway www.netpath.org...
Null TGF-beta Receptor Signaling Pathway View Gene Set 0.0003541 739 0.003364 2 From NetPath for TGF-beta Receptor Signaling Pathway www.netpath.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-4 Signaling Pathway View Gene Set 0.0004929 301 0.009859 1 From NetPath for IL-4 Signaling Pathway www.netpath.org...
Null Androgen Receptor Signaling Pathway View Gene Set 0.002073 586 0.02073 2 From NetPath for Androgen Receptor Signaling Pathway www.netpath.org...
Null EGFR1 Signaling Pathway View Gene Set 0.003371 253 0.02247 3 From NetPath for EGFR1 Signaling Pathway www.netpath.org...
Null TGF-beta Receptor Signaling Pathway View Gene Set 0.006815 1296 0.02726 4 From NetPath for TGF-beta Receptor Signaling Pathway www.netpath.org...
Null TNF-alpha Signaling Pathway View Gene Set 0.006611 863 0.02726 4 From NetPath for TNF-alpha 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 0.0004906 113 0.01177 1 From NetPath for TNFalpha www.netpath.org...

Gene Set Collection: hprdManual.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 TGF_beta_Receptor View Gene Set 0.0002308 399 0.004385 1 From NetPath for TGF_beta_Receptor www.netpath.org...

Gene Set Collection: hprdManual.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 TGF_beta_Receptor View Gene Set 0.0001952 594 0.004685 1 From NetPath for TGF_beta_Receptor www.netpath.org...
Null TNFalpha View Gene Set 0.0008049 121 0.009659 2 From NetPath for TNFalpha www.netpath.org...
Null IL4 View Gene Set 0.001369 269 0.01095 3 From NetPath for IL4 www.netpath.org...