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Coexpression cluster:C234

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Full id: C234_oral_epidermoid_malignant_cervical_ductal_lung_keratoacanthoma



Phase1 CAGE Peaks

  Short description
Hg19::chr10:101445599..101445602,+ p@chr10:101445599..101445602
+
Hg19::chr10:101445609..101445620,+ p@chr10:101445609..101445620
+
Hg19::chr10:54259251..54259258,+ p@chr10:54259251..54259258
+
Hg19::chr10:54259346..54259353,+ p@chr10:54259346..54259353
+
Hg19::chr10:54259376..54259387,+ p@chr10:54259376..54259387
+
Hg19::chr10:54259403..54259416,+ p@chr10:54259403..54259416
+
Hg19::chr10:54339875..54339879,+ p@chr10:54339875..54339879
+
Hg19::chr10:54367116..54367120,+ p@chr10:54367116..54367120
+
Hg19::chr11:119725484..119725509,+ p@chr11:119725484..119725509
+
Hg19::chr12:57570902..57570937,+ p@chr12:57570902..57570937
+
Hg19::chr12:79323118..79323147,+ p@chr12:79323118..79323147
+
Hg19::chr15:22921497..22921508,+ p9@CYFIP1
Hg19::chr15:40531454..40531469,+ p5@PAK6
Hg19::chr15:40531729..40531738,+ p15@PAK6
Hg19::chr15:79327658..79327669,- p@chr15:79327658..79327669
-
Hg19::chr15:79327671..79327679,- p@chr15:79327671..79327679
-
Hg19::chr15:99866695..99866740,+ p5@LRRC28
Hg19::chr16:2213530..2213556,+ p7@TRAF7
Hg19::chr16:56368957..56368963,+ p@chr16:56368957..56368963
+
Hg19::chr16:57935418..57935429,- p@chr16:57935418..57935429
-
Hg19::chr16:57935435..57935447,- p@chr16:57935435..57935447
-
Hg19::chr16:57935516..57935527,- p@chr16:57935516..57935527
-
Hg19::chr16:57935528..57935532,- -
p@chr16:57935528..57935532
Hg19::chr16:88355328..88355348,+ p@chr16:88355328..88355348
+
Hg19::chr17:39675882..39675894,- p@chr17:39675882..39675894
-
Hg19::chr17:39675898..39675905,- p@chr17:39675898..39675905
-
Hg19::chr17:39675950..39675974,- p@chr17:39675950..39675974
-
Hg19::chr19:10665857..10665900,- p@chr19:10665857..10665900
-
Hg19::chr1:96208925..96208927,+ p@chr1:96208925..96208927
+
Hg19::chr22:38146987..38147008,+ p5@TRIOBP
Hg19::chr2:180446392..180446403,- p@chr2:180446392..180446403
-
Hg19::chr2:61242118..61242125,- p@chr2:61242118..61242125
-
Hg19::chr2:61242126..61242129,- p@chr2:61242126..61242129
-
Hg19::chr2:61242131..61242134,- p@chr2:61242131..61242134
-
Hg19::chr3:123452821..123452832,- p@chr3:123452821..123452832
-
Hg19::chr3:59175564..59175565,+ p@chr3:59175564..59175565
+
Hg19::chr3:59175568..59175581,+ p@chr3:59175568..59175581
+
Hg19::chr3:59175679..59175715,+ p@chr3:59175679..59175715
+
Hg19::chr4:12213410..12213424,- p@chr4:12213410..12213424
-
Hg19::chr4:71388662..71388695,+ p@chr4:71388662..71388695
+
Hg19::chr5:150951027..150951036,- p@chr5:150951027..150951036
-
Hg19::chr5:150951045..150951053,- p@chr5:150951045..150951053
-
Hg19::chr6:85050384..85050396,+ p@chr6:85050384..85050396
+
Hg19::chr6:85050405..85050417,+ p@chr6:85050405..85050417
+
Hg19::chr6:97169224..97169250,- p@chr6:97169224..97169250
-
Hg19::chr7:48039803..48039815,- p3@SUN3
Hg19::chr7:48039832..48039849,- p1@SUN3
Hg19::chr7:55177524..55177550,+ p10@EGFR
Hg19::chr7:56051493..56051514,+ p@chr7:56051493..56051514
+
Hg19::chr8:104890366..104890371,+ p@chr8:104890366..104890371
+
Hg19::chr8:119029396..119029403,- p@chr8:119029396..119029403
-
Hg19::chr8:41575054..41575088,- p@chr8:41575054..41575088
-
Hg19::chr8:71613745..71613750,- p@chr8:71613745..71613750
-
Hg19::chr9:135936829..135936855,+ p@chr9:135936829..135936855
+
Hg19::chr9:135936872..135936875,+ p6@CEL
Hg19::chr9:137272217..137272225,+ p@chr9:137272217..137272225
+
Hg19::chr9:98532044..98532064,+ p@chr9:98532044..98532064
+
Hg19::chr9:98532075..98532082,+ p@chr9:98532075..98532082
+
Hg19::chrX:105936968..105936975,+ p11@RNF128
Hg19::chrX:105936982..105936997,+ p6@RNF128


Enriched pathways on this co-expression cluster
Summary:


Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.
Analyst: Emmanuel Dimont

link to source dataset


data

p.valueFDRnGenesnPathwayName
3.37554285299587e-050.02136718625946393214Regulation of actin cytoskeleton (KEGG):04810



Enriched Gene Ontology terms on this co-expression cluster
Summary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter.
Analyst: Erik Arner



link to source dataset


data

GO IDGO nameFDR corrected p-value
GO:0043687post-translational protein modification0.00082997889119931
GO:0006464protein modification process0.00107200405349154
GO:0043412biopolymer modification0.00107200405349154
GO:0017048Rho GTPase binding0.00247625807933599
GO:0051015actin filament binding0.00295708866151386
GO:0032501multicellular organismal process0.00318135985201998
GO:0051246regulation of protein metabolic process0.00586455504111573
GO:0003779actin binding0.00586455504111573
GO:0017016Ras GTPase binding0.00607853526433533
GO:0031267small GTPase binding0.00607853526433533
GO:0051020GTPase binding0.00607853526433533
GO:0030047actin modification0.00607853526433533
GO:0044258intestinal lipid catabolic process0.00607853526433533
GO:0045159myosin II binding0.00607853526433533
GO:0044240multicellular organismal lipid catabolic process0.00607853526433533
GO:0004710MAP/ERK kinase kinase activity0.00607853526433533
GO:0051248negative regulation of protein metabolic process0.00623852478682341
GO:0008092cytoskeletal protein binding0.00668992561804517
GO:0044267cellular protein metabolic process0.00845473637666067
GO:0044260cellular macromolecule metabolic process0.00845473637666067
GO:0018350protein amino acid esterification0.00845473637666067
GO:0043006calcium-dependent phospholipase A2 activation0.00845473637666067
GO:0045860positive regulation of protein kinase activity0.00845473637666067
GO:0033674positive regulation of kinase activity0.00845473637666067
GO:0051347positive regulation of transferase activity0.00845647520355778
GO:0019538protein metabolic process0.00848128371102795
GO:0005515protein binding0.00857969337402409
GO:0004842ubiquitin-protein ligase activity0.00857969337402409
GO:0008639small protein conjugating enzyme activity0.00857969337402409
GO:0032429regulation of phospholipase A2 activity0.00857969337402409
GO:0032431activation of phospholipase A20.00857969337402409
GO:0032430positive regulation of phospholipase A2 activity0.00857969337402409
GO:0005006epidermal growth factor receptor activity0.00857969337402409
GO:0004771sterol esterase activity0.00857969337402409
GO:0005768endosome0.0103727594682946
GO:0030235nitric-oxide synthase regulator activity0.0105670098153156
GO:0009889regulation of biosynthetic process0.0105670098153156
GO:0065007biological regulation0.0105670098153156
GO:0017049GTP-Rho binding0.0105670098153156
GO:0031529ruffle organization and biogenesis0.0105670098153156
GO:0030669clathrin-coated endocytic vesicle membrane0.0105670098153156
GO:0030128clathrin coat of endocytic vesicle0.0105670098153156
GO:0009062fatty acid catabolic process0.0105670098153156
GO:0030122AP-2 adaptor complex0.0105670098153156
GO:0000185activation of MAPKKK activity0.0105670098153156
GO:0030157pancreatic juice secretion0.0105670098153156
GO:0045859regulation of protein kinase activity0.01159391976791
GO:0019787small conjugating protein ligase activity0.01159391976791
GO:0043549regulation of kinase activity0.01159391976791
GO:0030666endocytic vesicle membrane0.0115984429230449
GO:0051338regulation of transferase activity0.0115984429230449
GO:0043085positive regulation of catalytic activity0.0122082524778653
GO:0050999regulation of nitric-oxide synthase activity0.0123411361574347
GO:0048365Rac GTPase binding0.0123411361574347
GO:0045334clathrin-coated endocytic vesicle0.0123411361574347
GO:0048523negative regulation of cellular process0.0123411361574347
GO:0030299cholesterol absorption0.0123411361574347
GO:0035272exocrine system development0.0123411361574347
GO:0030032lamellipodium biogenesis0.0123411361574347
GO:0043410positive regulation of MAPKKK cascade0.0123411361574347
GO:0045429positive regulation of nitric oxide biosynthetic process0.0123411361574347
GO:0044241lipid digestion0.0123411361574347
GO:0017022myosin binding0.0123411361574347
GO:0048519negative regulation of biological process0.012675187205804
GO:0016881acid-amino acid ligase activity0.012675187205804
GO:0005737cytoplasm0.012675187205804
GO:0051205protein insertion into membrane0.012675187205804
GO:0006707cholesterol catabolic process0.012675187205804
GO:0016127sterol catabolic process0.012675187205804
GO:0019899enzyme binding0.0128068140604994
GO:0050892intestinal absorption0.0131305978956997
GO:0016054organic acid catabolic process0.0131305978956997
GO:0045428regulation of nitric oxide biosynthetic process0.0131305978956997
GO:0046395carboxylic acid catabolic process0.0131305978956997
GO:0051341regulation of oxidoreductase activity0.0155434250131146
GO:0043283biopolymer metabolic process0.0158624483417039
GO:0030132clathrin coat of coated pit0.0160591317186777
GO:0051668localization within membrane0.0160591317186777
GO:0042802identical protein binding0.0160591317186777
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0164614413104735
GO:0046903secretion0.0173924417206685
GO:0043408regulation of MAPKKK cascade0.017551154462669
GO:0017157regulation of exocytosis0.017551154462669
GO:0007202phospholipase C activation0.0182788488059503
GO:0042036negative regulation of cytokine biosynthetic process0.0182788488059503
GO:0006706steroid catabolic process0.0185464998780557
GO:0004806triacylglycerol lipase activity0.0185464998780557
GO:0030335positive regulation of cell migration0.0185464998780557
GO:0048675axon extension0.0185464998780557
GO:0031410cytoplasmic vesicle0.0185910089984781
GO:0050679positive regulation of epithelial cell proliferation0.0185910089984781
GO:0006641triacylglycerol metabolic process0.0185910089984781
GO:0004709MAP kinase kinase kinase activity0.0185910089984781
GO:0007589fluid secretion0.0185910089984781
GO:0031982vesicle0.0186677100515402
GO:0009892negative regulation of metabolic process0.0187235319239128
GO:0016043cellular component organization and biogenesis0.0187235319239128
GO:0022600digestive system process0.0188209308384392
GO:0048731system development0.019239974086359
GO:0051272positive regulation of cell motility0.019239974086359
GO:0044243multicellular organismal catabolic process0.019239974086359
GO:0040017positive regulation of locomotion0.019239974086359
GO:0051693actin filament capping0.019239974086359
GO:0051016barbed-end actin filament capping0.019239974086359
GO:0030835negative regulation of actin filament depolymerization0.019239974086359
GO:0030125clathrin vesicle coat0.019239974086359
GO:0030139endocytic vesicle0.019239974086359
GO:0006809nitric oxide biosynthetic process0.019239974086359
GO:0046209nitric oxide metabolic process0.019239974086359
GO:0030834regulation of actin filament depolymerization0.019239974086359
GO:0030042actin filament depolymerization0.019239974086359
GO:0044236multicellular organismal metabolic process0.019239974086359
GO:0030665clathrin coated vesicle membrane0.019239974086359
GO:0042327positive regulation of phosphorylation0.019239974086359
GO:0006638neutral lipid metabolic process0.019239974086359
GO:0006639acylglycerol metabolic process0.019239974086359
GO:0046486glycerolipid metabolic process0.0199028506092353
GO:0045937positive regulation of phosphate metabolic process0.0203815973892503
GO:0006662glycerol ether metabolic process0.0203815973892503
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0226283921998209
GO:0050789regulation of biological process0.0226283921998209
GO:0006512ubiquitin cycle0.0231655327028394
GO:0050678regulation of epithelial cell proliferation0.0236503549970233
GO:0007173epidermal growth factor receptor signaling pathway0.0255912361987488
GO:0050673epithelial cell proliferation0.0255912361987488
GO:0050790regulation of catalytic activity0.0270642111962022
GO:0019717synaptosome0.0274695750993926
GO:0019722calcium-mediated signaling0.0280091669531585
GO:0030027lamellipodium0.0291752041501888
GO:0048856anatomical structure development0.0291752041501888
GO:0016874ligase activity0.029626590944466
GO:0017148negative regulation of translation0.0299085397152955
GO:0022603regulation of anatomical structure morphogenesis0.0299085397152955
GO:0022604regulation of cell morphogenesis0.0299085397152955
GO:0008360regulation of cell shape0.0299085397152955
GO:0018108peptidyl-tyrosine phosphorylation0.0299085397152955
GO:0065009regulation of a molecular function0.0299566856550253
GO:0005905coated pit0.0299566856550253
GO:0001726ruffle0.0299566856550253
GO:0018212peptidyl-tyrosine modification0.0300886059507785
GO:0008064regulation of actin polymerization and/or depolymerization0.0300886059507785
GO:0019222regulation of metabolic process0.0300886059507785
GO:0031327negative regulation of cellular biosynthetic process0.0300886059507785
GO:0001932regulation of protein amino acid phosphorylation0.0300886059507785
GO:0033238regulation of amine metabolic process0.0300886059507785
GO:0051261protein depolymerization0.0300886059507785
GO:0030832regulation of actin filament length0.0300886059507785
GO:0006521regulation of amino acid metabolic process0.0300886059507785
GO:0004674protein serine/threonine kinase activity0.0301288214400606
GO:0032535regulation of cellular component size0.0301288214400606
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0301288214400606
GO:0044242cellular lipid catabolic process0.0305642797103058
GO:0030031cell projection biogenesis0.0314178431974939
GO:0030120vesicle coat0.0314178431974939
GO:0030662coated vesicle membrane0.0314306160342309
GO:0009890negative regulation of biosynthetic process0.0314306160342309
GO:0005770late endosome0.0314306160342309
GO:0051129negative regulation of cellular component organization and biogenesis0.0318407956846703
GO:0030131clathrin adaptor complex0.0322456909329477
GO:0030119AP-type membrane coat adaptor complex0.0326454008835614
GO:0051493regulation of cytoskeleton organization and biogenesis0.033363553798076
GO:0033043regulation of organelle organization and biogenesis0.033363553798076
GO:0044459plasma membrane part0.033363553798076
GO:0007275multicellular organismal development0.0337195370824305
GO:0019752carboxylic acid metabolic process0.0345307987301992
GO:0042035regulation of cytokine biosynthetic process0.0345307987301992
GO:0030334regulation of cell migration0.0345307987301992
GO:0006082organic acid metabolic process0.0345307987301992
GO:0008154actin polymerization and/or depolymerization0.034888185905067
GO:0044444cytoplasmic part0.0359544511748904
GO:0042325regulation of phosphorylation0.0359544511748904
GO:0048471perinuclear region of cytoplasm0.0359544511748904
GO:0043406positive regulation of MAP kinase activity0.0366442986191015
GO:0030118clathrin coat0.0366442986191015
GO:0042089cytokine biosynthetic process0.0369831395401929
GO:0042107cytokine metabolic process0.0372283403277171
GO:0051174regulation of phosphorus metabolic process0.0372283403277171
GO:0019220regulation of phosphate metabolic process0.0372283403277171
GO:0051270regulation of cell motility0.0372283403277171
GO:0009891positive regulation of biosynthetic process0.0373467125137524
GO:0032147activation of protein kinase activity0.0373467125137524
GO:0040012regulation of locomotion0.0379861184081674
GO:0031252leading edge0.0379861184081674
GO:0016567protein ubiquitination0.0380934180166467
GO:0040011locomotion0.0380934180166467
GO:0008201heparin binding0.0392226289753796
GO:0051345positive regulation of hydrolase activity0.0392226289753796
GO:0004702receptor signaling protein serine/threonine kinase activity0.0392853115748897
GO:0032446protein modification by small protein conjugation0.0392853115748897
GO:0043170macromolecule metabolic process0.0392853115748897
GO:0008203cholesterol metabolic process0.0394036592692397
GO:0000151ubiquitin ligase complex0.0416896941200092
GO:0065008regulation of biological quality0.0419631073177305
GO:0048522positive regulation of cellular process0.0419631073177305
GO:0001503ossification0.0430571056967989
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0430571056967989
GO:0031214biomineral formation0.0430571056967989
GO:0043405regulation of MAP kinase activity0.0452504293491098
GO:0016125sterol metabolic process0.0455024768032393
GO:0007586digestion0.0457519052151574
GO:0046849bone remodeling0.0459987536924159
GO:0051128regulation of cellular component organization and biogenesis0.0476585458323638
GO:0048518positive regulation of biological process0.0490445590213351
GO:0048771tissue remodeling0.0490445590213351
GO:0046982protein heterodimerization activity0.0490445590213351
GO:0030659cytoplasmic vesicle membrane0.0490445590213351
GO:0044433cytoplasmic vesicle part0.0497270655458818
GO:0003690double-stranded DNA binding0.0499453594652825



Enriched sample ontology terms on this co-expression cluster
Summary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji



links to source dataset

cell_data
uberon_data

disease_data

Cell Type
Ontology termp-valuen
epithelial cell of alimentary canal2.29e-1120
Uber Anatomy
Ontology termp-valuen
mucosa of oral region3.10e-504
respiratory system mucosa3.10e-504
neck3.81e-2110
mouth mucosa1.21e-1613
mucosa2.29e-1120
oral opening1.80e-1022
mouth2.67e-0829
stomodeum2.67e-0829
orifice5.81e-0736
Disease
Ontology termp-valuen
squamous cell carcinoma1.43e-1514


Overrepresented TFBS (DNA) motifs on this co-expression cluster
Summary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs

data

Novel motifs


JASPAR motifs
Motifs-log10(p-value)
MA0003.10.000291637
MA0004.10.2028
MA0006.10.0495356
MA0007.10.0145963
MA0009.11.13224
MA0014.12.40648e-05
MA0017.10.310725
MA0019.10.437282
MA0024.10.146446
MA0025.10.299942
MA0027.11.66118
MA0028.10.00306998
MA0029.10.157192
MA0030.10.459763
MA0031.10.116937
MA0038.10.999586
MA0040.10.160513
MA0041.10.0206872
MA0042.10.0153775
MA0043.10.208842
MA0046.10.584097
MA0048.10.112662
MA0050.10.365844
MA0051.10.630425
MA0052.11.51341
MA0055.10.000586332
MA0056.10
MA0057.10.00068919
MA0058.10.587459
MA0059.10.207159
MA0060.11.01739
MA0061.10.202501
MA0063.10
MA0066.10.0400007
MA0067.10.442801
MA0068.10.0609137
MA0069.10.199334
MA0070.10.192383
MA0071.10.294552
MA0072.10.554995
MA0073.10.0930573
MA0074.10.0385277
MA0076.10.00746275
MA0077.10.543642
MA0078.10.532313
MA0081.10.369786
MA0083.10.213446
MA0084.10.602392
MA0087.10.188122
MA0088.11.03546
MA0089.10
MA0090.10.261968
MA0091.10.206239
MA0092.10.159356
MA0093.10.384399
MA0095.10
MA0098.10
MA0100.10.043811
MA0101.10.00263019
MA0103.11.32508
MA0105.10.17498
MA0106.13.35916
MA0107.10.0512679
MA0108.20.115431
MA0109.10
MA0111.10.491686
MA0113.10.210051
MA0114.10.461975
MA0115.10.993103
MA0116.10.207045
MA0117.10.658194
MA0119.10.771548
MA0122.10.6988
MA0124.10.349309
MA0125.10.287016
MA0130.10
MA0131.10.269326
MA0132.10
MA0133.10
MA0135.10.228328
MA0136.10.0418532
MA0139.10.168517
MA0140.10.121617
MA0141.10.0947759
MA0142.10.682233
MA0143.11.70351
MA0144.13.47125
MA0145.11.88765
MA0146.10.993466
MA0147.10.119405
MA0148.10.0953439
MA0149.10.0272934
MA0062.20.0282275
MA0035.20.849045
MA0039.20.0385291
MA0138.20.0716075
MA0002.20.00550067
MA0137.21.57004
MA0104.20.10293
MA0047.20.40823
MA0112.20.394353
MA0065.20.364372
MA0150.14.15102
MA0151.10
MA0152.10.551972
MA0153.10.275019
MA0154.10.165438
MA0155.11.01648
MA0156.10.277572
MA0157.10.300508
MA0158.10
MA0159.11.23399
MA0160.10.105936
MA0161.10
MA0162.11.47251e-07
MA0163.10.00053525
MA0164.11.7643
MA0080.20.581946
MA0018.20.432694
MA0099.23.95798
MA0079.27.60816e-10
MA0102.20.635361
MA0258.10.52733
MA0259.10.0243485
MA0442.10


ENCODE TF ChIP-seq peak enrichment analysis
Summary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.
Analyst: Erik Arner



link to source dataset


data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POLR3A#11128211.30440366972480.01372141010153760.0483191836804397
STAT3#6774162.80519066590780.0001113085935504710.00154628334687652



Relative expression of the co-expression cluster
Summary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data