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Coexpression cluster:C894

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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
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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
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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

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

GO IDGO nameFDR corrected p-value
GO:0046511sphinganine biosynthetic process0.00576920244788202
GO:0006669sphinganine-1-phosphate biosynthetic process0.00576920244788202
GO:0006667sphinganine metabolic process0.00576920244788202
GO:0008481sphinganine kinase activity0.00576920244788202
GO:0006668sphinganine-1-phosphate metabolic process0.00576920244788202
GO:0004772sterol O-acyltransferase activity0.00576920244788202
GO:0046520sphingoid biosynthetic process0.0222457607846574
GO:0051693actin filament capping0.0305927686437621
GO:0051016barbed-end actin filament capping0.0305927686437621
GO:0030148sphingolipid biosynthetic process0.0305927686437621
GO:0030835negative regulation of actin filament depolymerization0.0305927686437621
GO:0030834regulation of actin filament depolymerization0.0305927686437621
GO:0030042actin filament depolymerization0.0305927686437621
GO:0044255cellular lipid metabolic process0.0311977777640363
GO:0004143diacylglycerol kinase activity0.0324737040564231
GO:0046519sphingoid metabolic process0.0324737040564231
GO:0008374O-acyltransferase activity0.0324737040564231
GO:0007205protein kinase C activation0.0324737040564231
GO:0001727lipid kinase activity0.0324737040564231
GO:0006629lipid metabolic process0.0324737040564231
GO:0008064regulation of actin polymerization and/or depolymerization0.0324737040564231
GO:0051261protein depolymerization0.0324737040564231
GO:0030832regulation of actin filament length0.0324737040564231
GO:0032535regulation of cellular component size0.0324737040564231
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0324737040564231
GO:0051129negative regulation of cellular component organization and biogenesis0.0333419790760655
GO:0048523negative regulation of cellular process0.0333419790760655
GO:0051493regulation of cytoskeleton organization and biogenesis0.0333419790760655
GO:0033043regulation of organelle organization and biogenesis0.0333419790760655
GO:0048519negative regulation of biological process0.0339362981913713
GO:0008154actin polymerization and/or depolymerization0.0339682814923601
GO:0006665sphingolipid metabolic process0.0366030174808241
GO:0032147activation of protein kinase activity0.0366030174808241
GO:0017016Ras GTPase binding0.038441991507084
GO:0008203cholesterol metabolic process0.038441991507084
GO:0031267small GTPase binding0.0396152345344609
GO:0005200structural constituent of cytoskeleton0.0396152345344609
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0399288269016283
GO:0016125sterol metabolic process0.0415466116649148
GO:0051020GTPase binding0.0417952136990352
GO:0051128regulation of cellular component organization and biogenesis0.0420313551711835
GO:0051248negative regulation of protein metabolic process0.042664293013026
GO:0046467membrane lipid biosynthetic process0.045260339858271



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>

Cell Type
Ontology termp-valuen
metabolising cell1.17e-0712
endopolyploid cell1.17e-0712
parenchymal cell1.17e-0712
polyploid cell1.17e-0712
hepatocyte1.17e-0712
embryonic stem cell3.51e-075
Disease
Ontology termp-valuen
carcinoma2.51e-13106
cell type cancer5.97e-13143


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

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

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

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553314.95727118232580.0008400100540424580.00633656988328929
FOXA2#317038.210154584221750.00467281236756890.0220525915434491
HDAC2#306645.9624978829450.002864271980786230.0155220891138093
HEY1#2346273.142308589082220.001258763462843770.00845808385099018
HNF4A#3172615.42152690863584.88730097228247e-072.29921092902797e-05
HNF4G#3174722.36377307612532.07633960554806e-091.78625067597886e-07
RXRA#625648.9220520618370.0006332213048085760.00519750077435577



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

This analysis result is provided for C0 - C305 clusters.

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