Coexpression cluster:C234

Full id: C234_oral_epidermoid_malignant_cervical_ductal_lung_keratoacanthoma

Phase1 CAGE Peaks

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<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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p.value	FDR	nGenes	nPathway	Name
3.37554285299587e-05	0.0213671862594639	3	214	Regulation of actin cytoskeleton (KEGG):04810

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0043687	post-translational protein modification	0.00082997889119931
GO:0006464	protein modification process	0.00107200405349154
GO:0043412	biopolymer modification	0.00107200405349154
GO:0017048	Rho GTPase binding	0.00247625807933599
GO:0051015	actin filament binding	0.00295708866151386
GO:0032501	multicellular organismal process	0.00318135985201998
GO:0051246	regulation of protein metabolic process	0.00586455504111573
GO:0003779	actin binding	0.00586455504111573
GO:0017016	Ras GTPase binding	0.00607853526433533
GO:0031267	small GTPase binding	0.00607853526433533
GO:0051020	GTPase binding	0.00607853526433533
GO:0030047	actin modification	0.00607853526433533
GO:0044258	intestinal lipid catabolic process	0.00607853526433533
GO:0045159	myosin II binding	0.00607853526433533
GO:0044240	multicellular organismal lipid catabolic process	0.00607853526433533
GO:0004710	MAP/ERK kinase kinase activity	0.00607853526433533
GO:0051248	negative regulation of protein metabolic process	0.00623852478682341
GO:0008092	cytoskeletal protein binding	0.00668992561804517
GO:0044267	cellular protein metabolic process	0.00845473637666067
GO:0044260	cellular macromolecule metabolic process	0.00845473637666067
GO:0018350	protein amino acid esterification	0.00845473637666067
GO:0043006	calcium-dependent phospholipase A2 activation	0.00845473637666067
GO:0045860	positive regulation of protein kinase activity	0.00845473637666067
GO:0033674	positive regulation of kinase activity	0.00845473637666067
GO:0051347	positive regulation of transferase activity	0.00845647520355778
GO:0019538	protein metabolic process	0.00848128371102795
GO:0005515	protein binding	0.00857969337402409
GO:0004842	ubiquitin-protein ligase activity	0.00857969337402409
GO:0008639	small protein conjugating enzyme activity	0.00857969337402409
GO:0032429	regulation of phospholipase A2 activity	0.00857969337402409
GO:0032431	activation of phospholipase A2	0.00857969337402409
GO:0032430	positive regulation of phospholipase A2 activity	0.00857969337402409
GO:0005006	epidermal growth factor receptor activity	0.00857969337402409
GO:0004771	sterol esterase activity	0.00857969337402409
GO:0005768	endosome	0.0103727594682946
GO:0030235	nitric-oxide synthase regulator activity	0.0105670098153156
GO:0009889	regulation of biosynthetic process	0.0105670098153156
GO:0065007	biological regulation	0.0105670098153156
GO:0017049	GTP-Rho binding	0.0105670098153156
GO:0031529	ruffle organization and biogenesis	0.0105670098153156
GO:0030669	clathrin-coated endocytic vesicle membrane	0.0105670098153156
GO:0030128	clathrin coat of endocytic vesicle	0.0105670098153156
GO:0009062	fatty acid catabolic process	0.0105670098153156
GO:0030122	AP-2 adaptor complex	0.0105670098153156
GO:0000185	activation of MAPKKK activity	0.0105670098153156
GO:0030157	pancreatic juice secretion	0.0105670098153156
GO:0045859	regulation of protein kinase activity	0.01159391976791
GO:0019787	small conjugating protein ligase activity	0.01159391976791
GO:0043549	regulation of kinase activity	0.01159391976791
GO:0030666	endocytic vesicle membrane	0.0115984429230449
GO:0051338	regulation of transferase activity	0.0115984429230449
GO:0043085	positive regulation of catalytic activity	0.0122082524778653
GO:0050999	regulation of nitric-oxide synthase activity	0.0123411361574347
GO:0048365	Rac GTPase binding	0.0123411361574347
GO:0045334	clathrin-coated endocytic vesicle	0.0123411361574347
GO:0048523	negative regulation of cellular process	0.0123411361574347
GO:0030299	cholesterol absorption	0.0123411361574347
GO:0035272	exocrine system development	0.0123411361574347
GO:0030032	lamellipodium biogenesis	0.0123411361574347
GO:0043410	positive regulation of MAPKKK cascade	0.0123411361574347
GO:0045429	positive regulation of nitric oxide biosynthetic process	0.0123411361574347
GO:0044241	lipid digestion	0.0123411361574347
GO:0017022	myosin binding	0.0123411361574347
GO:0048519	negative regulation of biological process	0.012675187205804
GO:0016881	acid-amino acid ligase activity	0.012675187205804
GO:0005737	cytoplasm	0.012675187205804
GO:0051205	protein insertion into membrane	0.012675187205804
GO:0006707	cholesterol catabolic process	0.012675187205804
GO:0016127	sterol catabolic process	0.012675187205804
GO:0019899	enzyme binding	0.0128068140604994
GO:0050892	intestinal absorption	0.0131305978956997
GO:0016054	organic acid catabolic process	0.0131305978956997
GO:0045428	regulation of nitric oxide biosynthetic process	0.0131305978956997
GO:0046395	carboxylic acid catabolic process	0.0131305978956997
GO:0051341	regulation of oxidoreductase activity	0.0155434250131146
GO:0043283	biopolymer metabolic process	0.0158624483417039
GO:0030132	clathrin coat of coated pit	0.0160591317186777
GO:0051668	localization within membrane	0.0160591317186777
GO:0042802	identical protein binding	0.0160591317186777
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0164614413104735
GO:0046903	secretion	0.0173924417206685
GO:0043408	regulation of MAPKKK cascade	0.017551154462669
GO:0017157	regulation of exocytosis	0.017551154462669
GO:0007202	phospholipase C activation	0.0182788488059503
GO:0042036	negative regulation of cytokine biosynthetic process	0.0182788488059503
GO:0006706	steroid catabolic process	0.0185464998780557
GO:0004806	triacylglycerol lipase activity	0.0185464998780557
GO:0030335	positive regulation of cell migration	0.0185464998780557
GO:0048675	axon extension	0.0185464998780557
GO:0031410	cytoplasmic vesicle	0.0185910089984781
GO:0050679	positive regulation of epithelial cell proliferation	0.0185910089984781
GO:0006641	triacylglycerol metabolic process	0.0185910089984781
GO:0004709	MAP kinase kinase kinase activity	0.0185910089984781
GO:0007589	fluid secretion	0.0185910089984781
GO:0031982	vesicle	0.0186677100515402
GO:0009892	negative regulation of metabolic process	0.0187235319239128
GO:0016043	cellular component organization and biogenesis	0.0187235319239128
GO:0022600	digestive system process	0.0188209308384392
GO:0048731	system development	0.019239974086359
GO:0051272	positive regulation of cell motility	0.019239974086359
GO:0044243	multicellular organismal catabolic process	0.019239974086359
GO:0040017	positive regulation of locomotion	0.019239974086359
GO:0051693	actin filament capping	0.019239974086359
GO:0051016	barbed-end actin filament capping	0.019239974086359
GO:0030835	negative regulation of actin filament depolymerization	0.019239974086359
GO:0030125	clathrin vesicle coat	0.019239974086359
GO:0030139	endocytic vesicle	0.019239974086359
GO:0006809	nitric oxide biosynthetic process	0.019239974086359
GO:0046209	nitric oxide metabolic process	0.019239974086359
GO:0030834	regulation of actin filament depolymerization	0.019239974086359
GO:0030042	actin filament depolymerization	0.019239974086359
GO:0044236	multicellular organismal metabolic process	0.019239974086359
GO:0030665	clathrin coated vesicle membrane	0.019239974086359
GO:0042327	positive regulation of phosphorylation	0.019239974086359
GO:0006638	neutral lipid metabolic process	0.019239974086359
GO:0006639	acylglycerol metabolic process	0.019239974086359
GO:0046486	glycerolipid metabolic process	0.0199028506092353
GO:0045937	positive regulation of phosphate metabolic process	0.0203815973892503
GO:0006662	glycerol ether metabolic process	0.0203815973892503
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0226283921998209
GO:0050789	regulation of biological process	0.0226283921998209
GO:0006512	ubiquitin cycle	0.0231655327028394
GO:0050678	regulation of epithelial cell proliferation	0.0236503549970233
GO:0007173	epidermal growth factor receptor signaling pathway	0.0255912361987488
GO:0050673	epithelial cell proliferation	0.0255912361987488
GO:0050790	regulation of catalytic activity	0.0270642111962022
GO:0019717	synaptosome	0.0274695750993926
GO:0019722	calcium-mediated signaling	0.0280091669531585
GO:0030027	lamellipodium	0.0291752041501888
GO:0048856	anatomical structure development	0.0291752041501888
GO:0016874	ligase activity	0.029626590944466
GO:0017148	negative regulation of translation	0.0299085397152955
GO:0022603	regulation of anatomical structure morphogenesis	0.0299085397152955
GO:0022604	regulation of cell morphogenesis	0.0299085397152955
GO:0008360	regulation of cell shape	0.0299085397152955
GO:0018108	peptidyl-tyrosine phosphorylation	0.0299085397152955
GO:0065009	regulation of a molecular function	0.0299566856550253
GO:0005905	coated pit	0.0299566856550253
GO:0001726	ruffle	0.0299566856550253
GO:0018212	peptidyl-tyrosine modification	0.0300886059507785
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0300886059507785
GO:0019222	regulation of metabolic process	0.0300886059507785
GO:0031327	negative regulation of cellular biosynthetic process	0.0300886059507785
GO:0001932	regulation of protein amino acid phosphorylation	0.0300886059507785
GO:0033238	regulation of amine metabolic process	0.0300886059507785
GO:0051261	protein depolymerization	0.0300886059507785
GO:0030832	regulation of actin filament length	0.0300886059507785
GO:0006521	regulation of amino acid metabolic process	0.0300886059507785
GO:0004674	protein serine/threonine kinase activity	0.0301288214400606
GO:0032535	regulation of cellular component size	0.0301288214400606
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0301288214400606
GO:0044242	cellular lipid catabolic process	0.0305642797103058
GO:0030031	cell projection biogenesis	0.0314178431974939
GO:0030120	vesicle coat	0.0314178431974939
GO:0030662	coated vesicle membrane	0.0314306160342309
GO:0009890	negative regulation of biosynthetic process	0.0314306160342309
GO:0005770	late endosome	0.0314306160342309
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0318407956846703
GO:0030131	clathrin adaptor complex	0.0322456909329477
GO:0030119	AP-type membrane coat adaptor complex	0.0326454008835614
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.033363553798076
GO:0033043	regulation of organelle organization and biogenesis	0.033363553798076
GO:0044459	plasma membrane part	0.033363553798076
GO:0007275	multicellular organismal development	0.0337195370824305
GO:0019752	carboxylic acid metabolic process	0.0345307987301992
GO:0042035	regulation of cytokine biosynthetic process	0.0345307987301992
GO:0030334	regulation of cell migration	0.0345307987301992
GO:0006082	organic acid metabolic process	0.0345307987301992
GO:0008154	actin polymerization and/or depolymerization	0.034888185905067
GO:0044444	cytoplasmic part	0.0359544511748904
GO:0042325	regulation of phosphorylation	0.0359544511748904
GO:0048471	perinuclear region of cytoplasm	0.0359544511748904
GO:0043406	positive regulation of MAP kinase activity	0.0366442986191015
GO:0030118	clathrin coat	0.0366442986191015
GO:0042089	cytokine biosynthetic process	0.0369831395401929
GO:0042107	cytokine metabolic process	0.0372283403277171
GO:0051174	regulation of phosphorus metabolic process	0.0372283403277171
GO:0019220	regulation of phosphate metabolic process	0.0372283403277171
GO:0051270	regulation of cell motility	0.0372283403277171
GO:0009891	positive regulation of biosynthetic process	0.0373467125137524
GO:0032147	activation of protein kinase activity	0.0373467125137524
GO:0040012	regulation of locomotion	0.0379861184081674
GO:0031252	leading edge	0.0379861184081674
GO:0016567	protein ubiquitination	0.0380934180166467
GO:0040011	locomotion	0.0380934180166467
GO:0008201	heparin binding	0.0392226289753796
GO:0051345	positive regulation of hydrolase activity	0.0392226289753796
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0392853115748897
GO:0032446	protein modification by small protein conjugation	0.0392853115748897
GO:0043170	macromolecule metabolic process	0.0392853115748897
GO:0008203	cholesterol metabolic process	0.0394036592692397
GO:0000151	ubiquitin ligase complex	0.0416896941200092
GO:0065008	regulation of biological quality	0.0419631073177305
GO:0048522	positive regulation of cellular process	0.0419631073177305
GO:0001503	ossification	0.0430571056967989
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0430571056967989
GO:0031214	biomineral formation	0.0430571056967989
GO:0043405	regulation of MAP kinase activity	0.0452504293491098
GO:0016125	sterol metabolic process	0.0455024768032393
GO:0007586	digestion	0.0457519052151574
GO:0046849	bone remodeling	0.0459987536924159
GO:0051128	regulation of cellular component organization and biogenesis	0.0476585458323638
GO:0048518	positive regulation of biological process	0.0490445590213351
GO:0048771	tissue remodeling	0.0490445590213351
GO:0046982	protein heterodimerization activity	0.0490445590213351
GO:0030659	cytoplasmic vesicle membrane	0.0490445590213351
GO:0044433	cytoplasmic vesicle part	0.0497270655458818
GO:0003690	double-stranded DNA binding	0.0499453594652825

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
endodermal cell	4.00e-12	59
epithelial cell	4.43e-12	254
endo-epithelial cell	5.07e-11	43
epithelial cell of alimentary canal	1.51e-08	21

Uber Anatomy

Ontology term	p-value	n
head	3.55e-13	123
anterior region of body	1.45e-12	129
craniocervical region	1.45e-12	129
endoderm-derived structure	4.32e-12	169
endoderm	4.32e-12	169
presumptive endoderm	4.32e-12	169
organ	8.64e-12	511
ectoderm-derived structure	1.07e-11	169
ectoderm	5.61e-11	173
presumptive ectoderm	5.61e-11	173
digestive system	1.02e-09	155
digestive tract	1.02e-09	155
primitive gut	1.02e-09	155
brain	1.55e-09	69
future brain	1.55e-09	69
organism subdivision	9.23e-09	365
central nervous system	1.12e-08	82
regional part of brain	2.01e-08	59
regional part of nervous system	2.21e-08	94
nervous system	2.21e-08	94
neural tube	2.67e-08	57
neural rod	2.67e-08	57
future spinal cord	2.67e-08	57
neural keel	2.67e-08	57
regional part of forebrain	5.49e-08	41
forebrain	5.49e-08	41
future forebrain	5.49e-08	41
mixed endoderm/mesoderm-derived structure	1.55e-07	130
neural plate	2.16e-07	86
presumptive neural plate	2.16e-07	86
anterior neural tube	2.21e-07	42
subdivision of digestive tract	2.61e-07	129
endodermal part of digestive tract	2.61e-07	129
endo-epithelium	4.05e-07	82
multi-tissue structure	6.93e-07	347
telencephalon	7.49e-07	34
cerebral hemisphere	9.56e-07	32

Disease

Ontology term	p-value	n
carcinoma	5.03e-16	106
cell type cancer	1.46e-15	143
cancer	1.79e-10	235
disease of cellular proliferation	2.61e-10	239
squamous cell carcinoma	2.81e-09	14

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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

TF	#promoters	Enrichment	p-value	q-value
POLR3A#11128	2	11.3044036697248	0.0137214101015376	0.0483191836804397
STAT3#6774	16	2.8051906659078	0.000111308593550471	0.00154628334687652

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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