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Coexpression cluster:C4684: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281298972764876!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327692964726075
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281298972764876!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327692964726075
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}}
}}

Revision as of 16:53, 26 November 2012


Full id: C4684_Smooth_lung_Fibroblast_mesenchymal_Chondrocyte_basal_mesodermal



Phase1 CAGE Peaks

Hg19::chr7:33945106..33945116,+p3@BMPER
Hg19::chr7:33945132..33945160,+p1@BMPER
Hg19::chr7:33945169..33945180,+p4@BMPER


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
paraxial mesoderm1.12e-1972
presumptive paraxial mesoderm1.12e-1972
somite2.90e-1971
presomitic mesoderm2.90e-1971
presumptive segmental plate2.90e-1971
dermomyotome2.90e-1971
trunk paraxial mesoderm2.90e-1971
dense mesenchyme tissue4.15e-1973
epithelial vesicle2.03e-1678
skeletal muscle tissue2.21e-1662
striated muscle tissue2.21e-1662
myotome2.21e-1662
multilaminar epithelium2.67e-1683
muscle tissue4.22e-1664
musculature4.22e-1664
musculature of body4.22e-1664
splanchnic layer of lateral plate mesoderm2.83e-1483
artery8.10e-1442
arterial blood vessel8.10e-1442
arterial system8.10e-1442
systemic artery2.19e-1333
systemic arterial system2.19e-1333
tube1.01e-12192
integument1.03e-1146
integumental system1.03e-1146
structure with developmental contribution from neural crest2.84e-11132
epithelial tube open at both ends4.14e-1159
blood vessel4.14e-1159
blood vasculature4.14e-1159
vascular cord4.14e-1159
trunk mesenchyme6.54e-11122
primary circulatory organ1.42e-1027
multi-cellular organism2.87e-10656
heart3.01e-1024
primitive heart tube3.01e-1024
primary heart field3.01e-1024
anterior lateral plate mesoderm3.01e-1024
heart tube3.01e-1024
heart primordium3.01e-1024
cardiac mesoderm3.01e-1024
cardiogenic plate3.01e-1024
heart rudiment3.01e-1024
skin of body3.65e-1041
epithelium2.10e-09306
vessel2.42e-0968
multi-tissue structure2.81e-09342
epithelial tube2.99e-09117
cell layer5.68e-09309
blood vessel smooth muscle7.21e-0910
arterial system smooth muscle7.21e-0910
artery smooth muscle tissue7.21e-0910
aorta smooth muscle tissue7.21e-0910
anatomical conduit8.38e-09240
mesenchyme3.00e-08160
entire embryonic mesenchyme3.00e-08160
smooth muscle tissue1.02e-0715
circulatory system1.42e-07112
anatomical system1.55e-07624
anatomical group1.99e-07625
surface structure2.03e-0799
cardiovascular system3.66e-07109
vasculature5.03e-0778
vascular system5.03e-0778


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
CTCF#1066435.360256373075030.0064925092527670.0281298972764876
E2F1#186934.907389214879320.008460985347239390.0327692964726075



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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