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Coexpression cluster:C3509: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324599364023192
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324599364023192
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}}
}}

Revision as of 16:10, 26 November 2012


Full id: C3509_Fibroblast_Keratocytes_Myoblast_tridermal_Smooth_optic_embryonic



Phase1 CAGE Peaks

Hg19::chr15:71146436..71146447,-p3@LARP6
Hg19::chr15:71146461..71146475,-p2@LARP6
Hg19::chr15:71146480..71146531,-p1@LARP6


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
cell layer2.78e-20309
epithelium7.62e-20306
multi-tissue structure1.16e-17342
dense mesenchyme tissue4.00e-1673
paraxial mesoderm7.30e-1672
presumptive paraxial mesoderm7.30e-1672
somite9.59e-1671
presomitic mesoderm9.59e-1671
presumptive segmental plate9.59e-1671
dermomyotome9.59e-1671
trunk paraxial mesoderm9.59e-1671
anatomical cluster1.07e-15373
epithelial vesicle2.06e-1578
skeletal muscle tissue3.57e-1562
striated muscle tissue3.57e-1562
myotome3.57e-1562
anatomical conduit6.08e-15240
tube1.10e-14192
multilaminar epithelium1.88e-1483
muscle tissue4.00e-1464
musculature4.00e-1464
musculature of body4.00e-1464
structure with developmental contribution from neural crest5.35e-14132
mesenchyme1.41e-13160
entire embryonic mesenchyme1.41e-13160
multi-cellular organism3.80e-13656
artery9.62e-1342
arterial blood vessel9.62e-1342
arterial system9.62e-1342
organism subdivision1.04e-12264
trunk mesenchyme5.48e-12122
splanchnic layer of lateral plate mesoderm8.24e-1283
anatomical system1.40e-11624
trunk1.40e-11199
systemic artery1.41e-1133
systemic arterial system1.41e-1133
anatomical group2.61e-11625
vasculature3.00e-1178
vascular system3.00e-1178
epithelial tube open at both ends1.02e-1059
blood vessel1.02e-1059
blood vasculature1.02e-1059
vascular cord1.02e-1059
unilaminar epithelium9.48e-10148
vessel1.05e-0968
epithelial tube1.39e-09117
circulatory system3.91e-09112
cardiovascular system8.99e-09109
neural plate4.26e-0882
presumptive neural plate4.26e-0882
neurectoderm5.53e-0886
embryo9.28e-08592
ectoderm-derived structure1.98e-07171
ectoderm1.98e-07171
presumptive ectoderm1.98e-07171
developing anatomical structure3.91e-07581
ecto-epithelium5.08e-07104
brain6.69e-0768
future brain6.69e-0768
nervous system7.12e-0789


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
E2F1#186934.907389214879320.008460985347239390.0324599364023192



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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