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Coexpression cluster:C3963: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.16e-34!365;UBERON:0000119!3.30e-28!312;UBERON:0000483!5.12e-27!309;UBERON:0000468!1.44e-23!659;UBERON:0000481!2.98e-22!347;UBERON:0005256!2.89e-20!143;UBERON:0000467!6.10e-20!625;UBERON:0000480!1.16e-19!626;UBERON:0002100!6.67e-17!216;UBERON:0003102!4.19e-15!95;UBERON:0000922!6.50e-15!612;UBERON:0004111!3.20e-14!241;UBERON:0002050!4.81e-14!605;UBERON:0005423!4.81e-14!605;UBERON:0000923!5.23e-14!604;UBERON:0005291!5.23e-14!604;UBERON:0006598!5.23e-14!604;UBERON:0002532!5.23e-14!604;UBERON:0000477!1.43e-13!286;UBERON:0000914!3.58e-13!83;UBERON:0002329!3.58e-13!83;UBERON:0003077!3.58e-13!83;UBERON:0003059!3.58e-13!83;UBERON:0007282!3.58e-13!83;UBERON:0009618!3.58e-13!83;UBERON:0007285!3.58e-13!83;UBERON:0003104!4.40e-13!238;UBERON:0009142!4.40e-13!238;UBERON:0000064!9.51e-13!219;UBERON:0002199!4.57e-12!45;UBERON:0002416!4.57e-12!45;UBERON:0004290!4.76e-12!70;UBERON:0000062!6.55e-12!511;UBERON:0000025!7.58e-12!194;UBERON:0000486!2.83e-11!82;UBERON:0003914!9.94e-11!118;UBERON:0002097!2.25e-10!40;UBERON:0004211!9.35e-10!16;UBERON:0001285!9.35e-10!16;UBERON:0007684!9.35e-10!16;UBERON:0003220!9.35e-10!16;UBERON:0004208!9.35e-10!16;UBERON:0000490!1.05e-09!138;UBERON:0006555!6.20e-09!17;UBERON:0005103!6.20e-09!17;UBERON:0000083!6.20e-09!17;UBERON:0009201!6.20e-09!17;UBERON:0004819!6.20e-09!17;UBERON:0006553!6.20e-09!17;UBERON:0003074!6.20e-09!17;UBERON:0003060!6.20e-09!17;UBERON:0001134!6.69e-09!61;UBERON:0002036!6.69e-09!61;UBERON:0003082!6.69e-09!61;UBERON:0003064!7.72e-09!37;UBERON:0002385!1.52e-08!63;UBERON:0001015!1.52e-08!63;UBERON:0000383!1.52e-08!63;UBERON:0001225!3.04e-08!13;UBERON:0008987!3.04e-08!13;UBERON:0000080!3.46e-08!18;UBERON:0002120!3.46e-08!18;UBERON:0004875!3.46e-08!18;UBERON:0005721!3.46e-08!18;UBERON:0005754!3.46e-08!18;UBERON:0007297!3.46e-08!18;UBERON:0009773!5.58e-08!12;UBERON:0001231!5.58e-08!12;UBERON:0004810!5.58e-08!12;UBERON:0004876!8.61e-08!20;UBERON:0001008!1.12e-07!45;UBERON:0006554!1.12e-07!44;UBERON:0002049!1.31e-07!79;UBERON:0007798!1.31e-07!79;UBERON:0000033!1.35e-07!123;UBERON:0004121!1.77e-07!169;UBERON:0001851!1.79e-07!16;UBERON:0000924!3.77e-07!173;UBERON:0006601!3.77e-07!173;UBERON:0000353!3.91e-07!17;UBERON:0009569!8.03e-07!113;UBERON:0004872!9.27e-07!84
|ontology_enrichment_uberon=UBERON:0000475!7.16e-34!365;UBERON:0000119!3.30e-28!312;UBERON:0000483!5.12e-27!309;UBERON:0000468!1.44e-23!659;UBERON:0000481!2.98e-22!347;UBERON:0005256!2.89e-20!143;UBERON:0000467!6.10e-20!625;UBERON:0000480!1.16e-19!626;UBERON:0002100!6.67e-17!216;UBERON:0003102!4.19e-15!95;UBERON:0000922!6.50e-15!612;UBERON:0004111!3.20e-14!241;UBERON:0002050!4.81e-14!605;UBERON:0005423!4.81e-14!605;UBERON:0000923!5.23e-14!604;UBERON:0005291!5.23e-14!604;UBERON:0006598!5.23e-14!604;UBERON:0002532!5.23e-14!604;UBERON:0000477!1.43e-13!286;UBERON:0000914!3.58e-13!83;UBERON:0002329!3.58e-13!83;UBERON:0003077!3.58e-13!83;UBERON:0003059!3.58e-13!83;UBERON:0007282!3.58e-13!83;UBERON:0009618!3.58e-13!83;UBERON:0007285!3.58e-13!83;UBERON:0003104!4.40e-13!238;UBERON:0009142!4.40e-13!238;UBERON:0000064!9.51e-13!219;UBERON:0002199!4.57e-12!45;UBERON:0002416!4.57e-12!45;UBERON:0004290!4.76e-12!70;UBERON:0000062!6.55e-12!511;UBERON:0000025!7.58e-12!194;UBERON:0000486!2.83e-11!82;UBERON:0003914!9.94e-11!118;UBERON:0002097!2.25e-10!40;UBERON:0004211!9.35e-10!16;UBERON:0001285!9.35e-10!16;UBERON:0007684!9.35e-10!16;UBERON:0003220!9.35e-10!16;UBERON:0004208!9.35e-10!16;UBERON:0000490!1.05e-09!138;UBERON:0006555!6.20e-09!17;UBERON:0005103!6.20e-09!17;UBERON:0000083!6.20e-09!17;UBERON:0009201!6.20e-09!17;UBERON:0004819!6.20e-09!17;UBERON:0006553!6.20e-09!17;UBERON:0003074!6.20e-09!17;UBERON:0003060!6.20e-09!17;UBERON:0001134!6.69e-09!61;UBERON:0002036!6.69e-09!61;UBERON:0003082!6.69e-09!61;UBERON:0003064!7.72e-09!37;UBERON:0002385!1.52e-08!63;UBERON:0001015!1.52e-08!63;UBERON:0000383!1.52e-08!63;UBERON:0001225!3.04e-08!13;UBERON:0008987!3.04e-08!13;UBERON:0000080!3.46e-08!18;UBERON:0002120!3.46e-08!18;UBERON:0004875!3.46e-08!18;UBERON:0005721!3.46e-08!18;UBERON:0005754!3.46e-08!18;UBERON:0007297!3.46e-08!18;UBERON:0009773!5.58e-08!12;UBERON:0001231!5.58e-08!12;UBERON:0004810!5.58e-08!12;UBERON:0004876!8.61e-08!20;UBERON:0001008!1.12e-07!45;UBERON:0006554!1.12e-07!44;UBERON:0002049!1.31e-07!79;UBERON:0007798!1.31e-07!79;UBERON:0000033!1.35e-07!123;UBERON:0004121!1.77e-07!169;UBERON:0001851!1.79e-07!16;UBERON:0000924!3.77e-07!173;UBERON:0006601!3.77e-07!173;UBERON:0000353!3.91e-07!17;UBERON:0009569!8.03e-07!113;UBERON:0004872!9.27e-07!84
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}}
}}

Revision as of 19:35, 8 August 2012


Full id: C3963_Mesenchymal_Smooth_Fibroblast_Alveolar_Keratocytes_Hair_Renal



Phase1 CAGE Peaks

Hg19::chr1:27320176..27320200,+p1@TRNP1
Hg19::chr1:27320224..27320235,+p3@TRNP1
Hg19::chr1:27320382..27320395,+p2@TRNP1


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
organism subdivision7.16e-34365
cell layer3.30e-28312
epithelium5.12e-27309
multi-cellular organism1.44e-23659
multi-tissue structure2.98e-22347
trunk mesenchyme2.89e-20143
anatomical system6.10e-20625
anatomical group1.16e-19626
trunk6.67e-17216
surface structure4.19e-1595
embryo6.50e-15612
anatomical conduit3.20e-14241
embryonic structure4.81e-14605
developing anatomical structure4.81e-14605
germ layer5.23e-14604
embryonic tissue5.23e-14604
presumptive structure5.23e-14604
epiblast (generic)5.23e-14604
anatomical cluster1.43e-13286
somite3.58e-1383
paraxial mesoderm3.58e-1383
presomitic mesoderm3.58e-1383
presumptive segmental plate3.58e-1383
trunk paraxial mesoderm3.58e-1383
presumptive paraxial mesoderm3.58e-1383
mesenchyme4.40e-13238
entire embryonic mesenchyme4.40e-13238
organ part9.51e-13219
integument4.57e-1245
integumental system4.57e-1245
dermomyotome4.76e-1270
organ6.55e-12511
tube7.58e-12194
multilaminar epithelium2.83e-1182
epithelial tube9.94e-11118
skin of body2.25e-1040
nephron epithelium9.35e-1016
nephron9.35e-1016
uriniferous tubule9.35e-1016
metanephric mesenchyme9.35e-1016
nephrogenic mesenchyme9.35e-1016
unilaminar epithelium1.05e-09138
excretory tube6.20e-0917
mesonephric epithelium6.20e-0917
mesonephric tubule6.20e-0917
nephric duct6.20e-0917
kidney epithelium6.20e-0917
renal duct6.20e-0917
mesonephric duct6.20e-0917
pronephric duct6.20e-0917
skeletal muscle tissue6.69e-0961
striated muscle tissue6.69e-0961
myotome6.69e-0961
intermediate mesoderm7.72e-0937
muscle tissue1.52e-0863
musculature1.52e-0863
musculature of body1.52e-0863
cortex of kidney3.04e-0813
renal parenchyma3.04e-0813
mesonephros3.46e-0818
pronephros3.46e-0818
nephrogenic cord3.46e-0818
pronephric mesoderm3.46e-0818
rostral part of nephrogenic cord3.46e-0818
presumptive pronephric mesoderm3.46e-0818
renal tubule5.58e-0812
nephron tubule5.58e-0812
nephron tubule epithelium5.58e-0812
urogenital ridge8.61e-0820
renal system1.12e-0745
urinary system structure1.12e-0744
vasculature1.31e-0779
vascular system1.31e-0779
head1.35e-07123
ectoderm-derived structure1.77e-07169
cortex1.79e-0716


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

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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