Coexpression cluster:C137

Full id: C137_large_ductal_melanoma_cervical_Endothelial_Smooth_chronic

Phase1 CAGE Peaks

Hg19::chr11:17555398..17555410,-	p9@USH1C
Hg19::chr11:17555415..17555420,-	p11@USH1C
Hg19::chr11:17555421..17555441,-	p6@USH1C
Hg19::chr12:131856235..131856282,-	p@chr12:131856235..131856282 -
Hg19::chr12:40426483..40426524,-	p@chr12:40426483..40426524 -
Hg19::chr12:70944095..70944107,+	p@chr12:70944095..70944107 +
Hg19::chr13:46786138..46786153,+	p2@LRRC63
Hg19::chr14:88452908..88452916,-	p@chr14:88452908..88452916 -
Hg19::chr14:88452922..88452929,-	p@chr14:88452922..88452929 -
Hg19::chr14:88452944..88452960,-	p@chr14:88452944..88452960 -
Hg19::chr15:22550789..22550806,+	p@chr15:22550789..22550806 +
Hg19::chr15:22550810..22550816,+	p@chr15:22550810..22550816 +
Hg19::chr15:91143571..91143582,+	p@chr15:91143571..91143582 +
Hg19::chr16:3332452..3332454,+	p@chr16:3332452..3332454 +
Hg19::chr16:57832004..57832027,-	p4@KIFC3
Hg19::chr16:57832028..57832042,-	p10@KIFC3
Hg19::chr16:65159735..65159744,-	p@chr16:65159735..65159744 -
Hg19::chr16:65159769..65159787,-	p@chr16:65159769..65159787 -
Hg19::chr16:65432589..65432593,+	p@chr16:65432589..65432593 +
Hg19::chr16:82662683..82662690,-	p@chr16:82662683..82662690 -
Hg19::chr17:53809214..53809228,-	p5@TMEM100
Hg19::chr17:53809233..53809251,-	p3@TMEM100
Hg19::chr17:66511224..66511241,+	p29@PRKAR1A
Hg19::chr17:9716257..9716264,-	p@chr17:9716257..9716264 -
Hg19::chr17:9739681..9739708,+	p5@GLP2R
Hg19::chr17:9739716..9739725,+	p13@GLP2R
Hg19::chr17:9739727..9739738,+	p11@GLP2R
Hg19::chr18:5478350..5478363,-	p10@EPB41L3
Hg19::chr18:5478399..5478403,-	p24@EPB41L3
Hg19::chr18:5540365..5540373,-	p22@EPB41L3
Hg19::chr18:61368086..61368120,+	p@chr18:61368086..61368120 +
Hg19::chr18:61370192..61370197,+	p1@SERPINB11
Hg19::chr18:67562993..67563000,-	p@chr18:67562993..67563000 -
Hg19::chr18:67563022..67563032,-	p@chr18:67563022..67563032 -
Hg19::chr19:46665277..46665280,-	p@chr19:46665277..46665280 -
Hg19::chr19:46684088..46684108,-	p@chr19:46684088..46684108 -
Hg19::chr19:46684114..46684142,-	p@chr19:46684114..46684142 -
Hg19::chr1:154699181..154699196,+	p@chr1:154699181..154699196 +
Hg19::chr1:15653306..15653329,+	p8@FHAD1
Hg19::chr1:15653374..15653410,+	p5@FHAD1
Hg19::chr1:15653436..15653448,+	p12@FHAD1
Hg19::chr1:156783663..156783673,-	p11@SH2D2A
Hg19::chr1:156785210..156785223,-	p10@SH2D2A
Hg19::chr1:156785242..156785247,-	p19@SH2D2A
Hg19::chr1:156785292..156785301,-	p13@SH2D2A
Hg19::chr1:156786243..156786257,-	p6@SH2D2A
Hg19::chr1:188856517..188856523,-	p1@ENST00000414765
Hg19::chr1:188856567..188856573,-	p2@ENST00000414765
Hg19::chr1:188856590..188856595,-	p4@ENST00000414765
Hg19::chr1:188856977..188857009,-	p3@ENST00000414765
Hg19::chr1:188857554..188857562,-	p@chr1:188857554..188857562 -
Hg19::chr1:188861179..188861222,-	p@chr1:188861179..188861222 -
Hg19::chr1:188874798..188874820,+	p1@ENST00000445072
Hg19::chr1:234565260..234565271,-	p@chr1:234565260..234565271 -
Hg19::chr1:246469346..246469359,-	p7@SMYD3
Hg19::chr1:246469406..246469412,-	p18@SMYD3
Hg19::chr1:246887738..246887749,+	p7@SCCPDH
Hg19::chr1:246887780..246887791,+	p6@SCCPDH
Hg19::chr1:54665916..54665927,+	p2@MRPL37
Hg19::chr1:68927028..68927036,-	p@chr1:68927028..68927036 -
Hg19::chr21:11130568..11130575,+	p@chr21:11130568..11130575 +
Hg19::chr2:115929667..115929677,+	p@chr2:115929667..115929677 +
Hg19::chr2:228190043..228190054,+	p5@MFF
Hg19::chr2:228190066..228190086,+	p4@MFF
Hg19::chr3:16739396..16739405,-	p5@ENST00000426218
Hg19::chr3:189838995..189839000,-	p31@LEPREL1
Hg19::chr3:189839367..189839371,-	p16@LEPREL1
Hg19::chr3:189840026..189840048,-	p10@LEPREL1
Hg19::chr3:189840061..189840073,-	p14@LEPREL1
Hg19::chr3:189840106..189840120,-	p18@LEPREL1
Hg19::chr3:63804973..63804980,+	p3@C3orf49
Hg19::chr3:63805017..63805035,+	p2@C3orf49
Hg19::chr3:63805044..63805054,+	p1@C3orf49
Hg19::chr4:103265976..103265993,-	p11@SLC39A8
Hg19::chr4:103266043..103266060,-	p12@SLC39A8
Hg19::chr4:103266068..103266091,-	p10@SLC39A8
Hg19::chr4:103266101..103266106,-	p20@SLC39A8
Hg19::chr4:159131359..159131372,+	p11@TMEM144
Hg19::chr4:159131486..159131501,+	p8@TMEM144
Hg19::chr4:40194268..40194278,+	p27@RHOH
Hg19::chr4:74586784..74586789,-	p@chr4:74586784..74586789 -
Hg19::chr5:119697827..119697855,+	p@chr5:119697827..119697855 +
Hg19::chr5:119697859..119697884,+	p@chr5:119697859..119697884 +
Hg19::chr5:136896379..136896398,-	p@chr5:136896379..136896398 -
Hg19::chr5:5558678..5558683,+	p@chr5:5558678..5558683 +
Hg19::chr5:57878034..57878045,+	p9@RAB3C
Hg19::chr5:59744572..59744583,-	p57@PDE4D
Hg19::chr5:59783574..59783584,+	p6@PART1
Hg19::chr6:1312753..1312800,+	p4@FOXQ1
Hg19::chr6:138060034..138060045,-	p1@ENST00000411615 p1@ENST00000419220
Hg19::chr6:138060103..138060111,-	p3@ENST00000411615 p3@ENST00000419220
Hg19::chr6:138060178..138060193,-	p2@ENST00000411615 p2@ENST00000419220
Hg19::chr6:145434485..145434492,+	p@chr6:145434485..145434492 +
Hg19::chr6:162477886..162477932,-	p@chr6:162477886..162477932 -
Hg19::chr6:166575975..166575983,-	p@chr6:166575975..166575983 -
Hg19::chr6:166579326..166579334,-	p@chr6:166579326..166579334 -
Hg19::chr6:166581324..166581327,-	p7@T
Hg19::chr6:166581333..166581349,-	p2@T
Hg19::chr6:166581938..166581955,-	p3@T
Hg19::chr6:166582133..166582149,-	p1@T
Hg19::chr6:22113567..22113578,+	p@chr6:22113567..22113578 +
Hg19::chr6:22113587..22113603,+	p@chr6:22113587..22113603 +
Hg19::chr6:22113608..22113630,+	p@chr6:22113608..22113630 +
Hg19::chr6:22113639..22113643,+	p@chr6:22113639..22113643 +
Hg19::chr6:33644021..33644058,+	p@chr6:33644021..33644058 +
Hg19::chr6:36952360..36952367,-	p@chr6:36952360..36952367 -
Hg19::chr7:151169194..151169198,-	p17@RHEB
Hg19::chr7:158225991..158225999,+	p@chr7:158225991..158225999 +
Hg19::chr7:158226043..158226065,+	p@chr7:158226043..158226065 +
Hg19::chr7:158237237..158237241,+	p@chr7:158237237..158237241 +
Hg19::chr7:158242968..158242975,+	p@chr7:158242968..158242975 +
Hg19::chr7:31938679..31938703,-	p@chr7:31938679..31938703 -
Hg19::chr7:32083456..32083492,-	p@chr7:32083456..32083492 -
Hg19::chr7:68735026..68735050,+	p@chr7:68735026..68735050 +
Hg19::chr7:68735078..68735090,+	p@chr7:68735078..68735090 +
Hg19::chr7:68735132..68735135,+	p@chr7:68735132..68735135 +
Hg19::chr7:68735137..68735150,+	p@chr7:68735137..68735150 +
Hg19::chr7:68735214..68735224,+	p@chr7:68735214..68735224 +
Hg19::chr8:129431377..129431384,-	p@chr8:129431377..129431384 -
Hg19::chr8:52307771..52307797,+	p@chr8:52307771..52307797 +
Hg19::chr9:138393091..138393107,+	p@chr9:138393091..138393107 +
Hg19::chr9:138393119..138393159,+	p@chr9:138393119..138393159 +
Hg19::chr9:138393171..138393178,+	p@chr9:138393171..138393178 +
Hg19::chr9:138393188..138393204,+	p@chr9:138393188..138393204 +
Hg19::chr9:138393225..138393257,+	p@chr9:138393225..138393257 +
Hg19::chr9:138393587..138393606,-	p8@C9orf116
Hg19::chr9:138393704..138393727,+	p@chr9:138393704..138393727 +
Hg19::chr9:138394283..138394314,+	p9@MRPS2
Hg19::chr9:33306373..33306392,+	p@chr9:33306373..33306392 +
Hg19::chr9:79009244..79009257,-	p4@RFK
Hg19::chrX:110341059..110341099,+	p@chrX:110341059..110341099 +
Hg19::chrX:142113711..142113717,+	p1@SPANXN4
Hg19::chrX:23803131..23803142,+	p7@SAT1

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:0005737	cytoplasm	0.0191544599457173
GO:0030046	parallel actin filament bundle formation	0.0435505411641322
GO:0048513	organ development	0.0435505411641322
GO:0047131	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity	0.0435505411641322
GO:0009231	riboflavin biosynthetic process	0.0435505411641322
GO:0042727	riboflavin and derivative biosynthetic process	0.0435505411641322
GO:0006771	riboflavin metabolic process	0.0435505411641322
GO:0004753	saccharopine dehydrogenase activity	0.0435505411641322
GO:0042726	riboflavin and derivative metabolic process	0.0435505411641322
GO:0004145	diamine N-acetyltransferase activity	0.0435505411641322
GO:0001917	photoreceptor inner segment	0.0435505411641322
GO:0008531	riboflavin kinase activity	0.0435505411641322
GO:0048598	embryonic morphogenesis	0.0460967290243841
GO:0044424	intracellular part	0.0460967290243841
GO:0009887	organ morphogenesis	0.0460967290243841
GO:0019797	procollagen-proline 3-dioxygenase activity	0.0460967290243841
GO:0031544	peptidyl-proline 3-dioxygenase activity	0.0460967290243841

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
embryo	4.10e-07	612
organ	4.63e-07	511
larynx	5.22e-07	9

Disease

Ontology term	p-value	n
disease of cellular proliferation	1.51e-09	239
cancer	7.82e-09	235
carcinoma	1.48e-07	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
CEBPB#1051	26	1.55826946068756	0.0140609214528899	0.0493467043791247
NR3C1#2908	18	2.02642421023394	0.00334943287737872	0.0172994125058383

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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