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Coexpression cluster:C1936: Difference between revisions

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|tf_chipseq_enrich=TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200085903909386!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000572109760538786
|tf_chipseq_enrich=TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200085903909386!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000572109760538786
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1936_Wilms_extraskeletal_Skeletal_uterus_cervix_lung_salivary



Phase1 CAGE Peaks

Hg19::chr4:148402078..148402099,+p4@EDNRA
Hg19::chr4:148402109..148402132,+p2@EDNRA
Hg19::chr4:148402212..148402230,+p3@EDNRA
Hg19::chr4:148402237..148402276,+p1@EDNRA
Hg19::chr4:148402291..148402302,+p5@EDNRA


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>

Cell Type
Ontology termp-valuen
fibroblast1.09e-0976
contractile cell8.03e-0959
muscle precursor cell2.20e-0858
myoblast2.20e-0858
multi-potent skeletal muscle stem cell2.20e-0858
muscle cell5.66e-0855
electrically responsive cell4.13e-0761
electrically active cell4.13e-0761
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.97e-24342
anatomical cluster9.76e-15373
multi-cellular organism1.01e-13656
adult organism1.40e-13114
dense mesenchyme tissue1.78e-1273
paraxial mesoderm4.33e-1272
presumptive paraxial mesoderm4.33e-1272
somite5.20e-1271
presomitic mesoderm5.20e-1271
presumptive segmental plate5.20e-1271
dermomyotome5.20e-1271
trunk paraxial mesoderm5.20e-1271
structure with developmental contribution from neural crest7.08e-12132
organism subdivision1.63e-11264
surface structure9.12e-1199
anatomical system1.07e-10624
cell layer1.42e-10309
anatomical group1.56e-10625
muscle tissue1.56e-1064
musculature1.56e-1064
musculature of body1.56e-1064
epithelial vesicle1.99e-1078
multilaminar epithelium3.54e-1083
skeletal muscle tissue6.87e-1062
striated muscle tissue6.87e-1062
myotome6.87e-1062
embryo1.07e-09592
epithelium1.20e-09306
developing anatomical structure1.59e-09581
embryonic structure2.39e-09564
tissue3.12e-09773
ectoderm-derived structure5.53e-09171
ectoderm5.53e-09171
presumptive ectoderm5.53e-09171
organ system subdivision5.77e-09223
germ layer7.48e-09560
germ layer / neural crest7.48e-09560
embryonic tissue7.48e-09560
presumptive structure7.48e-09560
germ layer / neural crest derived structure7.48e-09560
epiblast (generic)7.48e-09560
mesenchyme9.38e-09160
entire embryonic mesenchyme9.38e-09160
organ1.43e-07503
trunk mesenchyme3.06e-07122
anterior region of body3.31e-0762
craniocervical region3.31e-0762
neurectoderm3.61e-0786


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
TCF7L2#6934510.77017656313736.89693748574565e-060.000200085903909386
ZNF263#1012758.221841637010682.6606316672286e-050.000572109760538786



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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