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Coexpression cluster:C2831: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2831_Smooth_Fibroblast_cholangiocellular_osteoclastoma_basal_spindle_Ewing
|full_id=C2831_Smooth_Fibroblast_cholangiocellular_osteoclastoma_basal_spindle_Ewing
|id=C2831
|id=C2831

Revision as of 15:37, 12 September 2012


Full id: C2831_Smooth_Fibroblast_cholangiocellular_osteoclastoma_basal_spindle_Ewing



Phase1 CAGE Peaks

Hg19::chr5:83680192..83680209,-p5@EDIL3
Hg19::chr5:83680211..83680254,-p3@EDIL3
Hg19::chr5:83680261..83680270,-p10@EDIL3
Hg19::chr5:83680271..83680298,-p6@EDIL3


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 subdivision6.93e-18365
multi-tissue structure1.10e-15347
anatomical cluster2.82e-14286
multi-cellular organism4.23e-14659
somite7.12e-1383
paraxial mesoderm7.12e-1383
presomitic mesoderm7.12e-1383
presumptive segmental plate7.12e-1383
trunk paraxial mesoderm7.12e-1383
presumptive paraxial mesoderm7.12e-1383
skeletal muscle tissue5.38e-1261
striated muscle tissue5.38e-1261
myotome5.38e-1261
muscle tissue8.28e-1263
musculature8.28e-1263
musculature of body8.28e-1263
tube8.76e-12194
splanchnic layer of lateral plate mesoderm3.66e-1184
artery6.79e-1142
arterial blood vessel6.79e-1142
arterial system6.79e-1142
trunk mesenchyme7.14e-11143
dermomyotome9.28e-1170
cell layer2.53e-10312
epithelial tube5.74e-10118
epithelium5.78e-10309
anatomical conduit6.19e-10241
systemic artery9.18e-1033
systemic arterial system9.18e-1033
anatomical system1.31e-09625
anatomical group1.63e-09626
vasculature1.64e-0979
vascular system1.64e-0979
blood vessel5.39e-0960
epithelial tube open at both ends5.39e-0960
blood vasculature5.39e-0960
vascular cord5.39e-0960
central nervous system1.12e-0882
regional part of nervous system1.12e-0894
nervous system1.12e-0894
embryo1.24e-08612
trunk2.00e-08216
cardiovascular system4.27e-08110
ectoderm-derived structure5.03e-08169
head5.13e-08123
circulatory system5.33e-08113
ectoderm7.75e-08173
presumptive ectoderm7.75e-08173
multilaminar epithelium1.88e-0782
germ layer1.94e-07604
embryonic tissue1.94e-07604
presumptive structure1.94e-07604
epiblast (generic)1.94e-07604
embryonic structure1.95e-07605
developing anatomical structure1.95e-07605
brain4.67e-0769
future brain4.67e-0769
anterior region of body6.49e-07129
craniocervical region6.49e-07129
vessel7.82e-0769
mesenchyme8.99e-07238
entire embryonic mesenchyme8.99e-07238
heart9.83e-0724
primitive heart tube9.83e-0724
primary heart field9.83e-0724
anterior lateral plate mesoderm9.83e-0724
heart tube9.83e-0724
heart primordium9.83e-0724
cardiac mesoderm9.83e-0724
cardiogenic plate9.83e-0724
heart rudiment9.83e-0724


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
TAF1#687243.343046285745290.008005664898701650.0323181800608984



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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