Coexpression cluster:C255

Full id: C255_Wilms_leiomyoblastoma_kidney_adrenal_MCF7_epithelioid_Mast

Phase1 CAGE Peaks

Hg19::chr10:43867077..43867098,+	p1@FXYD4
Hg19::chr10:84983078..84983087,+	p@chr10:84983078..84983087 +
Hg19::chr11:121513919..121513924,-	p@chr11:121513919..121513924 -
Hg19::chr11:77792240..77792241,+	p@chr11:77792240..77792241 +
Hg19::chr11:77792301..77792328,+	p@chr11:77792301..77792328 +
Hg19::chr12:42983782..42983815,-	p2@PRICKLE1
Hg19::chr12:42983843..42983865,-	p3@PRICKLE1
Hg19::chr12:43946001..43946016,-	p1@ADAMTS20
Hg19::chr15:39561378..39561415,-	p@chr15:39561378..39561415 -
Hg19::chr15:88119982..88120003,+	p2@LINC00052
Hg19::chr15:88120158..88120161,+	p1@LINC00052
Hg19::chr15:88799370..88799383,-	p6@NTRK3
Hg19::chr16:80838418..80838432,-	p5@CDYL2
Hg19::chr16:80838441..80838473,-	p2@CDYL2
Hg19::chr16:80838479..80838508,-	p1@CDYL2
Hg19::chr17:41132410..41132418,-	p8@AARSD1
Hg19::chr19:46651474..46651514,+	p1@IGFL2
Hg19::chr19:50381565..50381605,-	p4@AKT1S1
Hg19::chr1:153517273..153517295,-	p5@S100A4
Hg19::chr1:172347750..172347761,+	p11@DNM3
Hg19::chr1:180601188..180601207,+	p2@XPR1
Hg19::chr1:180601215..180601233,+	p4@XPR1
Hg19::chr1:183387723..183387763,-	p7@NMNAT2
Hg19::chr1:201438498..201438583,-	p3@PHLDA3
Hg19::chr1:201532249..201532262,+	p@chr1:201532249..201532262 +
Hg19::chr1:201532269..201532289,+	p@chr1:201532269..201532289 +
Hg19::chr1:43387667..43387671,-	p@chr1:43387667..43387671 -
Hg19::chr1:62785019..62785032,-	p4@KANK4
Hg19::chr1:62902308..62902335,+	p9@USP1
Hg19::chr1:62902336..62902387,+	p2@USP1
Hg19::chr1:62902414..62902438,+	p5@USP1
Hg19::chr1:63213403..63213406,+	p@chr1:63213403..63213406 +
Hg19::chr1:69521584..69521593,+	p2@ENST00000425517
Hg19::chr20:42545244..42545247,-	p@chr20:42545244..42545247 -
Hg19::chr21:18218138..18218142,-	p@chr21:18218138..18218142 -
Hg19::chr2:139791638..139791647,+	p@chr2:139791638..139791647 +
Hg19::chr2:140592929..140592932,+	p@chr2:140592929..140592932 +
Hg19::chr3:47088671..47088676,-	p28@SETD2
Hg19::chr3:96532316..96532327,+	p@chr3:96532316..96532327 +
Hg19::chr3:96533452..96533467,+	p3@EPHA6
Hg19::chr5:103006456..103006466,+	p@chr5:103006456..103006466 +
Hg19::chr5:103012042..103012047,+	p@chr5:103012042..103012047 +
Hg19::chr5:159343481..159343528,+	p1@ADRA1B
Hg19::chr5:159343688..159343754,+	p2@ADRA1B
Hg19::chr5:159343995..159344006,+	p5@ADRA1B
Hg19::chr5:56247250..56247252,-	p@chr5:56247250..56247252 -
Hg19::chr5:56248032..56248039,-	p3@MIER3
Hg19::chr7:116070621..116070623,-	p@chr7:116070621..116070623 -
Hg19::chr7:139168434..139168465,-	p2@KLRG2
Hg19::chr9:15552504..15552550,+	p13@C9orf93
Hg19::chrX:13062697..13062745,-	p1@FAM9C

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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No results for this coexpression

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:0031330	negative regulation of cellular catabolic process	0.0243337650614231
GO:0045818	negative regulation of glycogen catabolic process	0.0243337650614231
GO:0045819	positive regulation of glycogen catabolic process	0.0243337650614231
GO:0031329	regulation of cellular catabolic process	0.0243337650614231
GO:0005981	regulation of glycogen catabolic process	0.0243337650614231
GO:0001987	vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure	0.0243337650614231
GO:0043278	response to morphine	0.0243337650614231
GO:0031331	positive regulation of cellular catabolic process	0.0243337650614231
GO:0014072	response to isoquinoline alkaloid	0.0243337650614231
GO:0001982	baroreceptor response to decreased systemic arterial blood pressure	0.0291923521403618
GO:0003099	positive regulation of the force of heart contraction by chemical signal	0.0291923521403618
GO:0001996	positive regulation of heart rate by epinephrine-norepinephrine	0.0291923521403618
GO:0048148	behavioral response to cocaine	0.0291923521403618
GO:0003057	regulation of the force of heart contraction by chemical signal	0.0291923521403618
GO:0001997	positive regulation of the force of heart contraction by epinephrine-norepinephrine	0.0291923521403618
GO:0004813	alanine-tRNA ligase activity	0.0298474661164654
GO:0045912	negative regulation of carbohydrate metabolic process	0.0298474661164654
GO:0010460	positive regulation of heart rate	0.0298474661164654
GO:0006419	alanyl-tRNA aminoacylation	0.0298474661164654
GO:0000309	nicotinamide-nucleotide adenylyltransferase activity	0.0298474661164654
GO:0042220	response to cocaine	0.0298474661164654
GO:0014073	response to tropane	0.0298474661164654
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.030184957028829
GO:0001978	carotid sinus baroreceptor feedback regulation of systemic arterial blood pressure	0.0312600309926838
GO:0003025	baroreceptor regulation of systemic arterial blood pressure	0.0312600309926838
GO:0001975	response to amphetamine	0.0312600309926838
GO:0014075	response to amine stimulus	0.0312600309926838
GO:0043526	neuroprotection	0.0312600309926838
GO:0019199	transmembrane receptor protein kinase activity	0.0321704466659882
GO:0004937	alpha1-adrenergic receptor activity	0.0321704466659882
GO:0043121	neurotrophin binding	0.0321704466659882
GO:0035265	organ growth	0.0321704466659882
GO:0045823	positive regulation of heart contraction	0.0321704466659882
GO:0001993	regulation of systemic arterial blood pressure by norepinephrine-epinephrine	0.0321704466659882
GO:0002027	regulation of heart rate	0.0347831181905141
GO:0005980	glycogen catabolic process	0.0347831181905141
GO:0009251	glucan catabolic process	0.0347831181905141
GO:0045913	positive regulation of carbohydrate metabolic process	0.0347831181905141
GO:0007512	adult heart development	0.0347831181905141
GO:0002026	regulation of the force of heart contraction	0.0347831181905141
GO:0009896	positive regulation of catabolic process	0.0347831181905141
GO:0001974	blood vessel remodeling	0.0347831181905141
GO:0003084	positive regulation of systemic arterial blood pressure	0.0347831181905141
GO:0008542	visual learning	0.0347831181905141
GO:0001976	regulation of systemic arterial blood pressure by neurological process	0.0364292713497891
GO:0006109	regulation of carbohydrate metabolic process	0.0364292713497891
GO:0000299	integral to membrane of membrane fraction	0.0364292713497891
GO:0043279	response to alkaloid	0.0364292713497891
GO:0009895	negative regulation of catabolic process	0.0393326162769219
GO:0004936	alpha-adrenergic receptor activity	0.0393326162769219
GO:0007632	visual behavior	0.0420102813890101
GO:0045777	positive regulation of blood pressure	0.0420102813890101
GO:0014070	response to organic cyclic substance	0.0444873434181894
GO:0001837	epithelial to mesenchymal transition	0.0444873434181894
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0454180426281821
GO:0003044	regulation of systemic arterial blood pressure mediated by a chemical signal	0.0467852967057092

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	2.06e-25	82
regional part of nervous system	3.38e-24	94
nervous system	3.38e-24	94
neural tube	1.09e-23	57
neural rod	1.09e-23	57
future spinal cord	1.09e-23	57
neural keel	1.09e-23	57
brain	6.64e-22	69
future brain	6.64e-22	69
regional part of brain	5.57e-20	59
ectoderm-derived structure	4.74e-19	169
multi-cellular organism	5.38e-19	659
neural plate	7.70e-19	86
presumptive neural plate	7.70e-19	86
anterior neural tube	1.47e-18	42
regional part of forebrain	3.75e-18	41
forebrain	3.75e-18	41
future forebrain	3.75e-18	41
ectoderm	1.42e-17	173
presumptive ectoderm	1.42e-17	173
gray matter	2.30e-17	34
brain grey matter	2.30e-17	34
telencephalon	6.32e-17	34
neurectoderm	1.17e-16	90
cerebral hemisphere	2.11e-16	32
regional part of telencephalon	2.47e-16	33
anatomical system	4.74e-16	625
anatomical group	1.15e-15	626
organ	1.23e-15	511
adult organism	1.31e-15	115
organ part	4.69e-15	219
cerebral cortex	5.16e-14	25
pallium	5.16e-14	25
head	1.87e-13	123
pre-chordal neural plate	7.88e-13	61
regional part of cerebral cortex	8.80e-13	22
anterior region of body	1.05e-12	129
craniocervical region	1.05e-12	129
embryo	1.88e-12	612
neocortex	3.26e-12	20
anatomical cluster	4.82e-11	286
embryonic structure	8.73e-11	605
developing anatomical structure	8.73e-11	605
tube	1.59e-10	194
germ layer	1.85e-10	604
embryonic tissue	1.85e-10	604
presumptive structure	1.85e-10	604
epiblast (generic)	1.85e-10	604
anatomical conduit	1.77e-09	241
organism subdivision	1.24e-08	365

Disease

Ontology term	p-value	n
cell type cancer	6.05e-09	143
carcinoma	2.47e-08	106

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
CTCF#10664	17	1.78675212435834	0.00900219480913783	0.0341300404280519

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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