Coexpression cluster:C576

Full id: C576_Hepatocyte_hepatocellular_liver_Intestinal_mature_breast_Prostate

Phase1 CAGE Peaks

Hg19::chr10:113987378..113987454,-	p@chr10:113987378..113987454 -
Hg19::chr10:7755243..7755254,-	p@chr10:7755243..7755254 -
Hg19::chr10:7773844..7773851,+	p@chr10:7773844..7773851 +
Hg19::chr12:57828432..57828442,+	p7@INHBC
Hg19::chr12:57828463..57828472,+	p9@INHBC
Hg19::chr16:85570675..85570678,+	p@chr16:85570675..85570678 +
Hg19::chr17:19437692..19437704,-	p1@AK127534
Hg19::chr17:7082861..7082882,-	p9@ASGR1
Hg19::chr1:21996247..21996270,-	p6@RAP1GAP
Hg19::chr2:20793103..20793113,-	p@chr2:20793103..20793113 -
Hg19::chr2:44066386..44066398,-	p6@ABCG5
Hg19::chr5:149516966..149516977,-	p8@PDGFRB
Hg19::chr5:32174797..32174803,-	p17@GOLPH3
Hg19::chr6:64231645..64231678,+	p6@PTP4A1
Hg19::chr8:144417558..144417572,-	p7@TOP1MT

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:0042493	response to drug	0.0221113997876872
GO:0006855	multidrug transport	0.0363522643590524
GO:0005017	platelet-derived growth factor receptor activity	0.0363522643590524
GO:0004873	asialoglycoprotein receptor activity	0.0363522643590524
GO:0004992	platelet activating factor receptor activity	0.0387711830818315
GO:0030299	cholesterol absorption	0.0458376287579303
GO:0003917	DNA topoisomerase type I activity	0.0458376287579303
GO:0044241	lipid digestion	0.0458376287579303
GO:0050892	intestinal absorption	0.0458376287579303
GO:0003918	DNA topoisomerase (ATP-hydrolyzing) activity	0.0458376287579303
GO:0005160	transforming growth factor beta receptor binding	0.0458376287579303
GO:0016020	membrane	0.0458376287579303
GO:0010212	response to ionizing radiation	0.0458376287579303
GO:0006268	DNA unwinding during replication	0.0458376287579303
GO:0006265	DNA topological change	0.0458376287579303
GO:0003916	DNA topoisomerase activity	0.0458376287579303
GO:0015893	drug transport	0.0458376287579303
GO:0032392	DNA geometric change	0.0458376287579303
GO:0032508	DNA duplex unwinding	0.0458376287579303
GO:0022600	digestive system process	0.0459595450544434
GO:0015238	drug transporter activity	0.0483613875409549
GO:0005021	vascular endothelial growth factor receptor activity	0.0483613875409549

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><br>

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Cell Type

Ontology term	p-value	n
metabolising cell	3.55e-46	12
endopolyploid cell	3.55e-46	12
parenchymal cell	3.55e-46	12
polyploid cell	3.55e-46	12
hepatocyte	3.55e-46	12
endodermal cell	9.15e-10	58

Uber Anatomy

Ontology term	p-value	n
liver	1.67e-56	19
digestive gland	1.67e-56	19
liver bud	1.67e-56	19
hepatic diverticulum	7.93e-49	22
liver primordium	7.93e-49	22
digestive tract diverticulum	1.03e-46	23
epithelial sac	5.45e-43	25
epithelium of foregut-midgut junction	5.45e-43	25
anatomical boundary	5.45e-43	25
hepatobiliary system	5.45e-43	25
foregut-midgut junction	5.45e-43	25
septum transversum	5.45e-43	25
sac	2.42e-41	26
exocrine gland	1.07e-34	31
exocrine system	1.07e-34	31
endocrine gland	9.61e-31	35
endocrine system	6.32e-24	45
gut epithelium	6.12e-20	54
abdomen element	6.12e-20	54
abdominal segment element	6.12e-20	54
gland	3.01e-18	59
abdominal segment of trunk	6.06e-18	60
abdomen	6.06e-18	60
endo-epithelium	4.14e-13	82
foregut	2.38e-12	87
trunk region element	1.29e-10	101
subdivision of trunk	1.48e-09	112
immaterial anatomical entity	3.86e-09	117
epithelial tube	3.86e-09	117
subdivision of digestive tract	5.54e-09	118
trunk mesenchyme	9.32e-09	122
digestive system	2.81e-07	145
digestive tract	2.81e-07	145
primitive gut	2.81e-07	145
unilaminar epithelium	3.55e-07	148

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	6	3.18845905032993	0.00708661775802942	0.02955157804076
EP300#2033	8	3.61276892065237	0.000545267193917108	0.00470949061077645
FOXA1#3169	5	3.69380658312848	0.00829376303603737	0.0326741726790157
FOXA2#3170	5	8.21015458422175	0.000234934965228373	0.00256442023761351
HDAC2#3066	5	4.47187341220875	0.00365865752308656	0.0184753182986963
HEY1#23462	12	3.23208883448457	1.10567306413993e-05	0.00028597174132172
HNF4A#3172	9	13.8793742177722	2.07194282394466e-09	1.78393764707301e-07
HNF4G#3174	10	19.1689483509645	6.57815993221828e-12	8.41931918089393e-10
RXRA#6256	6	8.0298468556533	5.16480117100425e-05	0.000878941941499939
SP1#6667	9	3.41902882688454	0.000283012712846588	0.00301085512040184
TCF7L2#6934	5	3.59005885437911	0.00934660680353175	0.0353038071592786

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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This analysis result is provided for C0 - C305 clusters.