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Coexpression cluster:C1874: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.48e-29!115;UBERON:0007100!3.38e-07!27;UBERON:0002616!5.27e-07!59
|ontology_enrichment_uberon=UBERON:0007023!2.48e-29!115;UBERON:0007100!3.38e-07!27;UBERON:0002616!5.27e-07!59
|tf_chipseq_enrich=CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.013850764327145!GTF2B#2959;2:12.7775319737297:0.0091993608955972:0.0347904132595334!THAP1#55145;2:12.5476578411405:0.00952843466738653:0.0358906548933235!ZNF143#7702;3:8.10052593133674:0.00362487051209098:0.0183348436367818
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}}
}}

Revision as of 11:50, 5 September 2012


Full id: C1874_left_Hepatocyte_liver_heart_Adipocyte_mature_small



Phase1 CAGE Peaks

Hg19::chr20:7238917..7238933,-p1@ENST00000428954
Hg19::chr3:48936246..48936268,-p2@SLC25A20
Hg19::chr3:48936272..48936353,-p1@SLC25A20
Hg19::chr4:159593418..159593517,+p1@ETFDH
Hg19::chr5:41213584..41213598,-p2@C6


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:0009054electron acceptor activity0.00558580461822105
GO:0005743mitochondrial inner membrane0.00558580461822105
GO:0004174electron-transferring-flavoprotein dehydrogenase activity0.00558580461822105
GO:0016649oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor0.00558580461822105
GO:0019866organelle inner membrane0.00558580461822105
GO:0031966mitochondrial membrane0.00678749457995214
GO:0005740mitochondrial envelope0.00678749457995214
GO:0005579membrane attack complex0.00764833106111847
GO:0044429mitochondrial part0.00898406663165033
GO:0031967organelle envelope0.00898406663165033
GO:0031975envelope0.00898406663165033
GO:0019835cytolysis0.011651512098125
GO:0006958complement activation, classical pathway0.017470065340674
GO:0005739mitochondrion0.017470065340674
GO:0002455humoral immune response mediated by circulating immunoglobulin0.017470065340674
GO:0006956complement activation0.0194054685455721
GO:0002541activation of plasma proteins during acute inflammatory response0.0194054685455721
GO:00515394 iron, 4 sulfur cluster binding0.0194054685455721
GO:0016064immunoglobulin mediated immune response0.0216155960363867
GO:0019724B cell mediated immunity0.0216155960363867
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0216155960363867
GO:0031090organelle membrane0.0223513859044162
GO:0002253activation of immune response0.0223513859044162
GO:0002449lymphocyte mediated immunity0.0223513859044162
GO:0006959humoral immune response0.0223513859044162
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0223513859044162
GO:0002250adaptive immune response0.0223513859044162
GO:0002443leukocyte mediated immunity0.0223513859044162
GO:0002526acute inflammatory response0.0223513859044162
GO:0050778positive regulation of immune response0.0223513859044162
GO:0002684positive regulation of immune system process0.0223513859044162
GO:0016021integral to membrane0.0223513859044162
GO:0031224intrinsic to membrane0.0223513859044162
GO:0051536iron-sulfur cluster binding0.0223513859044162
GO:0051540metal cluster binding0.0223513859044162
GO:0005319lipid transporter activity0.0223513859044162
GO:0046930pore complex0.0223513859044162
GO:0050776regulation of immune response0.0223513859044162
GO:0002682regulation of immune system process0.0223513859044162
GO:0051240positive regulation of multicellular organismal process0.0228788602740446
GO:0002252immune effector process0.0233802913039492
GO:0045087innate immune response0.0236507793913901
GO:0044425membrane part0.0270730510644044
GO:0009055electron carrier activity0.0498973553192995



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>


Cell Type
Ontology termp-valuen
fat cell8.41e-0815
Uber Anatomy
Ontology termp-valuen
adult organism2.48e-29115
primary circulatory organ3.38e-0727
regional part of brain5.27e-0759


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
CTBP2#1488225.08680013573130.002461438599678380.013850764327145
GTF2B#2959212.77753197372970.00919936089559720.0347904132595334
THAP1#55145212.54765784114050.009528434667386530.0358906548933235
ZNF143#770238.100525931336740.003624870512090980.0183348436367818



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.