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Coexpression cluster:C1277: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!7.05e-19!347;UBERON:0000468!6.14e-18!659;UBERON:0000477!1.49e-17!286;UBERON:0000475!2.28e-14!365;UBERON:0000467!9.93e-14!625;UBERON:0000480!1.88e-13!626;UBERON:0007023!2.87e-13!115;UBERON:0005256!8.38e-13!143;UBERON:0003104!2.62e-12!238;UBERON:0009142!2.62e-12!238;UBERON:0004111!1.14e-11!241;UBERON:0000119!7.48e-11!312;UBERON:0002100!9.27e-11!216;UBERON:0000483!1.44e-10!309;UBERON:0000490!6.59e-10!138;UBERON:0000025!1.15e-09!194;UBERON:0000062!1.37e-09!511;UBERON:0003914!1.90e-09!118;UBERON:0002385!2.22e-09!63;UBERON:0001015!2.22e-09!63;UBERON:0000383!2.22e-09!63;UBERON:0002050!1.02e-08!605;UBERON:0005423!1.02e-08!605;UBERON:0001134!1.45e-08!61;UBERON:0002036!1.45e-08!61;UBERON:0003082!1.45e-08!61;UBERON:0002107!1.53e-08!19;UBERON:0006925!1.53e-08!19;UBERON:0008836!1.53e-08!19;UBERON:0009856!1.54e-08!26;UBERON:0001048!1.58e-08!168;UBERON:0000922!1.64e-08!612;UBERON:0000923!1.77e-08!604;UBERON:0005291!1.77e-08!604;UBERON:0006598!1.77e-08!604;UBERON:0002532!1.77e-08!604;UBERON:0009854!3.14e-08!23;UBERON:0007499!4.71e-08!25;UBERON:0004290!7.69e-08!70;UBERON:0001007!8.29e-08!155;UBERON:0001555!8.29e-08!155;UBERON:0007026!8.29e-08!155;UBERON:0008835!9.77e-08!22;UBERON:0003894!9.77e-08!22;UBERON:0004921!1.26e-07!129;UBERON:0004185!1.26e-07!129;UBERON:0000914!1.75e-07!83;UBERON:0002329!1.75e-07!83;UBERON:0003077!1.75e-07!83;UBERON:0003059!1.75e-07!83;UBERON:0007282!1.75e-07!83;UBERON:0009618!1.75e-07!83;UBERON:0007285!1.75e-07!83;UBERON:0002368!5.13e-07!35;UBERON:0009497!5.73e-07!25;UBERON:0000015!5.73e-07!25;UBERON:0002423!5.73e-07!25;UBERON:0006235!5.73e-07!25;UBERON:0004161!5.73e-07!25;UBERON:0005057!7.45e-07!26;UBERON:0003929!8.14e-07!54
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}}
}}

Revision as of 17:05, 8 August 2012


Full id: C1277_Hepatocyte_mature_mesenchymal_smooth_bladder_normal_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr5:52083909..52083927,+p7@PELO
Hg19::chr5:52083929..52083940,+p12@PELO
Hg19::chr5:52083991..52084021,+p3@ITGA1
Hg19::chr5:52084023..52084051,+p2@ITGA1
Hg19::chr5:52084059..52084086,+p4@ITGA1
Hg19::chr5:52084087..52084115,+p5@ITGA1
Hg19::chr5:52084126..52084133,+p8@ITGA1


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:0045123cellular extravasation0.0155415249616414
GO:0030593neutrophil chemotaxis0.0223346942055352
GO:0005518collagen binding0.0223346942055352
GO:0030595leukocyte chemotaxis0.0223346942055352
GO:0050900leukocyte migration0.0240797902081608
GO:0009897external side of plasma membrane0.0305050789062747
GO:0008305integrin complex0.0305050789062747
GO:0007229integrin-mediated signaling pathway0.038793191786861
GO:0007160cell-matrix adhesion0.038793191786861
GO:0031589cell-substrate adhesion0.038793191786861
GO:0043235receptor complex0.038793191786861
GO:0042330taxis0.0409869718598991
GO:0006935chemotaxis0.0409869718598991
GO:0009986cell surface0.0409869718598991
GO:0007626locomotory behavior0.0467614554761341



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
non-terminally differentiated cell3.37e-09180
fat cell1.15e-0715
muscle precursor cell1.97e-0757
myoblast1.97e-0757
multi-potent skeletal muscle stem cell1.97e-0757
smooth muscle cell3.46e-0742
smooth muscle myoblast3.46e-0742
muscle cell3.96e-0754
fibroblast6.63e-0775
contractile cell8.89e-0759
Uber Anatomy
Ontology termp-valuen
multi-tissue structure7.05e-19347
multi-cellular organism6.14e-18659
anatomical cluster1.49e-17286
organism subdivision2.28e-14365
anatomical system9.93e-14625
anatomical group1.88e-13626
adult organism2.87e-13115
trunk mesenchyme8.38e-13143
mesenchyme2.62e-12238
entire embryonic mesenchyme2.62e-12238
anatomical conduit1.14e-11241
cell layer7.48e-11312
trunk9.27e-11216
epithelium1.44e-10309
unilaminar epithelium6.59e-10138
tube1.15e-09194
organ1.37e-09511
epithelial tube1.90e-09118
muscle tissue2.22e-0963
musculature2.22e-0963
musculature of body2.22e-0963
embryonic structure1.02e-08605
developing anatomical structure1.02e-08605
skeletal muscle tissue1.45e-0861
striated muscle tissue1.45e-0861
myotome1.45e-0861
liver1.53e-0819
digestive gland1.53e-0819
liver bud1.53e-0819
sac1.54e-0826
primordium1.58e-08168
embryo1.64e-08612
germ layer1.77e-08604
embryonic tissue1.77e-08604
presumptive structure1.77e-08604
epiblast (generic)1.77e-08604
digestive tract diverticulum3.14e-0823
epithelial sac4.71e-0825
dermomyotome7.69e-0870
digestive system8.29e-08155
digestive tract8.29e-08155
primitive gut8.29e-08155
hepatic diverticulum9.77e-0822
liver primordium9.77e-0822
subdivision of digestive tract1.26e-07129
endodermal part of digestive tract1.26e-07129
somite1.75e-0783
paraxial mesoderm1.75e-0783
presomitic mesoderm1.75e-0783
presumptive segmental plate1.75e-0783
trunk paraxial mesoderm1.75e-0783
presumptive paraxial mesoderm1.75e-0783
endocrine gland5.13e-0735
epithelium of foregut-midgut junction5.73e-0725
anatomical boundary5.73e-0725
hepatobiliary system5.73e-0725
foregut-midgut junction5.73e-0725
septum transversum5.73e-0725
immune organ7.45e-0726
gut epithelium8.14e-0754


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)

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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

No analysis results for this cluster

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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