Coexpression cluster:C894

Full id: C894_small_hepatoblastoma_colon_hepatocellular_liver_Intestinal_Prostate

Phase1 CAGE Peaks

Hg19::chr12:53497263..53497311,+	p1@SOAT2
Hg19::chr15:65337469..65337477,+	p9@OSTBETA
Hg19::chr15:65337671..65337680,+	p4@OSTBETA
Hg19::chr15:65337778..65337794,+	p3@OSTBETA
Hg19::chr17:28550048..28550058,-	p@chr17:28550048..28550058 -
Hg19::chr19:49128245..49128254,+	p13@SPHK2
Hg19::chr19:49128280..49128291,+	p9@SPHK2
Hg19::chr3:38029450..38029458,+	p12@VILL
Hg19::chr7:105517815..105517837,-	p@chr7:105517815..105517837 -

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:0046511	sphinganine biosynthetic process	0.00576920244788202
GO:0006669	sphinganine-1-phosphate biosynthetic process	0.00576920244788202
GO:0006667	sphinganine metabolic process	0.00576920244788202
GO:0008481	sphinganine kinase activity	0.00576920244788202
GO:0006668	sphinganine-1-phosphate metabolic process	0.00576920244788202
GO:0004772	sterol O-acyltransferase activity	0.00576920244788202
GO:0046520	sphingoid biosynthetic process	0.0222457607846574
GO:0051693	actin filament capping	0.0305927686437621
GO:0051016	barbed-end actin filament capping	0.0305927686437621
GO:0030148	sphingolipid biosynthetic process	0.0305927686437621
GO:0030835	negative regulation of actin filament depolymerization	0.0305927686437621
GO:0030834	regulation of actin filament depolymerization	0.0305927686437621
GO:0030042	actin filament depolymerization	0.0305927686437621
GO:0044255	cellular lipid metabolic process	0.0311977777640363
GO:0004143	diacylglycerol kinase activity	0.0324737040564231
GO:0046519	sphingoid metabolic process	0.0324737040564231
GO:0008374	O-acyltransferase activity	0.0324737040564231
GO:0007205	protein kinase C activation	0.0324737040564231
GO:0001727	lipid kinase activity	0.0324737040564231
GO:0006629	lipid metabolic process	0.0324737040564231
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0324737040564231
GO:0051261	protein depolymerization	0.0324737040564231
GO:0030832	regulation of actin filament length	0.0324737040564231
GO:0032535	regulation of cellular component size	0.0324737040564231
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0324737040564231
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0333419790760655
GO:0048523	negative regulation of cellular process	0.0333419790760655
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0333419790760655
GO:0033043	regulation of organelle organization and biogenesis	0.0333419790760655
GO:0048519	negative regulation of biological process	0.0339362981913713
GO:0008154	actin polymerization and/or depolymerization	0.0339682814923601
GO:0006665	sphingolipid metabolic process	0.0366030174808241
GO:0032147	activation of protein kinase activity	0.0366030174808241
GO:0017016	Ras GTPase binding	0.038441991507084
GO:0008203	cholesterol metabolic process	0.038441991507084
GO:0031267	small GTPase binding	0.0396152345344609
GO:0005200	structural constituent of cytoskeleton	0.0396152345344609
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0399288269016283
GO:0016125	sterol metabolic process	0.0415466116649148
GO:0051020	GTPase binding	0.0417952136990352
GO:0051128	regulation of cellular component organization and biogenesis	0.0420313551711835
GO:0051248	negative regulation of protein metabolic process	0.042664293013026
GO:0046467	membrane lipid biosynthetic process	0.045260339858271

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
metabolising cell	1.17e-07	12
endopolyploid cell	1.17e-07	12
parenchymal cell	1.17e-07	12
polyploid cell	1.17e-07	12
hepatocyte	1.17e-07	12
embryonic stem cell	3.51e-07	5

Uber Anatomy

Ontology term	p-value	n
subdivision of digestive tract	7.02e-16	129
endodermal part of digestive tract	7.02e-16	129
digestive system	2.76e-15	155
digestive tract	2.76e-15	155
primitive gut	2.76e-15	155
endoderm-derived structure	1.33e-12	169
endoderm	1.33e-12	169
presumptive endoderm	1.33e-12	169
mixed endoderm/mesoderm-derived structure	8.49e-12	130
gastrointestinal system	4.73e-11	35
intestine	7.45e-10	27
foregut	2.44e-08	98
gut epithelium	6.05e-08	54
epithelium of foregut-midgut junction	1.47e-07	25
anatomical boundary	1.47e-07	25
hepatobiliary system	1.47e-07	25
foregut-midgut junction	1.47e-07	25
septum transversum	1.47e-07	25
digestive tract diverticulum	2.20e-07	23
sac	3.34e-07	26
endo-epithelium	3.61e-07	82

Disease

Ontology term	p-value	n
carcinoma	2.51e-13	106
cell type cancer	5.97e-13	143

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
BHLHE40#8553	3	14.9572711823258	0.000840010054042458	0.00633656988328929
FOXA2#3170	3	8.21015458422175	0.0046728123675689	0.0220525915434491
HDAC2#3066	4	5.962497882945	0.00286427198078623	0.0155220891138093
HEY1#23462	7	3.14230858908222	0.00125876346284377	0.00845808385099018
HNF4A#3172	6	15.4215269086358	4.88730097228247e-07	2.29921092902797e-05
HNF4G#3174	7	22.3637730761253	2.07633960554806e-09	1.78625067597886e-07
RXRA#6256	4	8.922052061837	0.000633221304808576	0.00519750077435577

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.