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Coexpression cluster:C1629: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318843767116318!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146334078297009!STAT3#6774;3:6.31167899829254:0.00741117212246054:0.030610432859988
|tf_chipseq_enrich=RAD21#5885;3:6.2130203372738:0.00775105506881164:0.0318843767116318!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146334078297009!STAT3#6774;3:6.31167899829254:0.00741117212246054:0.030610432859988
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1629_hepatic_spindle_Fibroblast_Smooth_liposarcoma_papillary_Ciliary



Phase1 CAGE Peaks

Hg19::chr11:27721994..27722008,-p1@BDNF
Hg19::chr11:27722021..27722038,-p2@BDNF
Hg19::chr11:27723079..27723100,-p4@BDNF
Hg19::chr11:27723140..27723153,-p6@BDNF
Hg19::chr11:27723158..27723188,-p3@BDNF


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
dense mesenchyme tissue2.86e-1573
somite7.47e-1571
presomitic mesoderm7.47e-1571
presumptive segmental plate7.47e-1571
dermomyotome7.47e-1571
trunk paraxial mesoderm7.47e-1571
paraxial mesoderm8.24e-1572
presumptive paraxial mesoderm8.24e-1572
skeletal muscle tissue2.89e-1462
striated muscle tissue2.89e-1462
myotome2.89e-1462
epithelial vesicle6.07e-1478
muscle tissue6.09e-1464
musculature6.09e-1464
musculature of body6.09e-1464
artery1.54e-1242
arterial blood vessel1.54e-1242
arterial system1.54e-1242
multilaminar epithelium2.76e-1283
trunk mesenchyme3.20e-11122
systemic artery6.08e-1133
systemic arterial system6.08e-1133
multi-tissue structure5.19e-10342
mesenchyme1.24e-09160
entire embryonic mesenchyme1.24e-09160
organism subdivision1.43e-09264
unilaminar epithelium8.26e-09148
epithelium8.28e-09306
vasculature9.49e-0978
vascular system9.49e-0978
cell layer1.28e-08309
trunk1.63e-08199
epithelial tube open at both ends3.08e-0859
blood vessel3.08e-0859
blood vasculature3.08e-0859
vascular cord3.08e-0859
epithelial tube6.37e-08117
splanchnic layer of lateral plate mesoderm1.10e-0783
cardiovascular system1.45e-07109
smooth muscle tissue1.99e-0715
skin of body3.24e-0741
circulatory system3.82e-07112
anatomical cluster5.61e-07373
surface structure7.34e-0799


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
RAD21#588536.21302033727380.007751055068811640.0318843767116318
SMC3#912639.02695970695970.002650964449467550.0146334078297009
STAT3#677436.311678998292540.007411172122460540.030610432859988



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.