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Coexpression cluster:C4678: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.0080031929379412!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191152779507887
|tf_chipseq_enrich=SUZ12#23512;2:33.4105206073753:0.0011782676453603:0.0080031929379412!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191152779507887
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}}
}}

Revision as of 16:53, 26 November 2012


Full id: C4678_Smooth_Mesothelial_glioma_mesenchymal_Renal_liposarcoma_Hepatic



Phase1 CAGE Peaks

Hg19::chr7:27157834..27157879,-p@chr7:27157834..27157879
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Hg19::chr7:27157924..27157950,-p@chr7:27157924..27157950
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Hg19::chr7:27157970..27157995,-p@chr7:27157970..27157995
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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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
subdivision of trunk4.19e-16112
nephron tubule epithelium8.58e-1610
trunk2.35e-15199
mesenchyme5.77e-15160
entire embryonic mesenchyme5.77e-15160
excretory tube5.94e-1516
kidney epithelium5.94e-1516
cavitated compound organ9.16e-1531
epithelial tube1.72e-14117
smooth muscle tissue2.65e-1415
nephron epithelium5.37e-1415
renal tubule5.37e-1415
nephron tubule5.37e-1415
nephron5.37e-1415
uriniferous tubule5.37e-1415
nephrogenic mesenchyme5.37e-1415
kidney1.35e-1326
kidney mesenchyme1.35e-1326
upper urinary tract1.35e-1326
kidney rudiment1.35e-1326
kidney field1.35e-1326
abdominal segment of trunk1.45e-1260
abdomen1.45e-1260
muscle tissue1.72e-1164
musculature1.72e-1164
musculature of body1.72e-1164
compound organ3.53e-1168
tube3.53e-11192
systemic artery1.03e-1033
systemic arterial system1.03e-1033
multi-tissue structure1.20e-10342
organism subdivision1.21e-10264
trunk region element2.28e-10101
skeletal muscle tissue3.04e-1062
striated muscle tissue3.04e-1062
myotome3.04e-1062
epithelial vesicle4.65e-1078
cortex of kidney8.23e-1012
renal parenchyma8.23e-1012
blood vessel smooth muscle1.20e-0910
arterial system smooth muscle1.20e-0910
artery smooth muscle tissue1.20e-0910
aorta smooth muscle tissue1.20e-0910
anatomical cluster2.93e-09373
immaterial anatomical entity4.35e-09117
trunk mesenchyme4.67e-09122
abdomen element5.54e-0954
abdominal segment element5.54e-0954
anatomical space1.61e-0895
artery3.39e-0842
arterial blood vessel3.39e-0842
arterial system3.39e-0842
somite5.08e-0871
presomitic mesoderm5.08e-0871
presumptive segmental plate5.08e-0871
dermomyotome5.08e-0871
trunk paraxial mesoderm5.08e-0871
paraxial mesoderm8.21e-0872
presumptive paraxial mesoderm8.21e-0872
epithelium8.71e-08306
posterior neural tube1.04e-0715
chordal neural plate1.04e-0715
dense mesenchyme tissue1.31e-0773
cell layer1.53e-07309
cortex2.12e-0715
parenchyma2.12e-0715
anatomical conduit2.44e-07240
urinary system structure5.14e-0747
aorta7.73e-0721
aortic system7.73e-0721
renal system9.10e-0748
Disease
Ontology termp-valuen
ovarian cancer9.42e-0714


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
SUZ12#23512233.41052060737530.00117826764536030.0080031929379412
USF1#739136.361499277207960.00388404057290560.0191152779507887



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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