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Coexpression cluster:C4249: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326421945506385!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058253325923247!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107423131903413!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061558716425352!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190820074039744!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422405295307139
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326421945506385!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058253325923247!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107423131903413!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061558716425352!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190820074039744!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422405295307139
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}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4249_Mesenchymal_mesenchymal_Cardiac_Chondrocyte_Myoblast_Preadipocyte_bone



Phase1 CAGE Peaks

Hg19::chr2:85980951..85981004,+p1@ATOH8
Hg19::chr2:85981008..85981025,+p7@ATOH8
Hg19::chr2:85981027..85981047,+p8@ATOH8


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
muscle tissue7.18e-1864
musculature7.18e-1864
musculature of body7.18e-1864
skeletal muscle tissue2.15e-1762
striated muscle tissue2.15e-1762
myotome2.15e-1762
splanchnic layer of lateral plate mesoderm1.90e-1583
anatomical cluster5.11e-15373
multi-tissue structure2.58e-14342
anatomical conduit7.48e-14240
vessel9.81e-1468
epithelial vesicle1.95e-1378
dense mesenchyme tissue5.67e-1373
paraxial mesoderm7.38e-1372
presumptive paraxial mesoderm7.38e-1372
somite7.38e-1371
presomitic mesoderm7.38e-1371
presumptive segmental plate7.38e-1371
dermomyotome7.38e-1371
trunk paraxial mesoderm7.38e-1371
epithelial tube open at both ends1.15e-1259
blood vessel1.15e-1259
blood vasculature1.15e-1259
vascular cord1.15e-1259
mesenchyme1.17e-12160
entire embryonic mesenchyme1.17e-12160
trunk mesenchyme1.26e-12122
artery5.08e-1242
arterial blood vessel5.08e-1242
arterial system5.08e-1242
tube2.44e-11192
vasculature2.48e-1178
vascular system2.48e-1178
epithelial tube2.65e-11117
epithelium1.80e-10306
multilaminar epithelium1.96e-1083
circulatory system4.53e-10112
systemic artery5.85e-1033
systemic arterial system5.85e-1033
cell layer6.16e-10309
unilaminar epithelium1.31e-09148
cardiovascular system1.46e-09109
multi-cellular organism3.88e-09656
trunk2.81e-08199
primary circulatory organ3.29e-0827
heart1.04e-0724
primitive heart tube1.04e-0724
primary heart field1.04e-0724
anterior lateral plate mesoderm1.04e-0724
heart tube1.04e-0724
heart primordium1.04e-0724
cardiac mesoderm1.04e-0724
cardiogenic plate1.04e-0724
heart rudiment1.04e-0724
adult organism6.69e-07114


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#186934.907389214879320.008460985347239390.0326421945506385
FOXA1#3169311.08141974938550.000734755275698670.0058253325923247
FOXA2#3170324.63046375266526.68983856509345e-050.00107423131903413
TCF7L2#6934310.77017656313730.0008003181298398380.0061558716425352
USF1#739136.361499277207960.00388404057290560.0190820074039744
USF2#7392312.99219738506960.0004558979393427810.00422405295307139



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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