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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1629_hepatic_spindle_Fibroblast_Smooth_liposarcoma_papillary_Ciliary
|full_id=C1629_hepatic_spindle_Fibroblast_Smooth_liposarcoma_papillary_Ciliary
|id=C1629
|id=C1629

Revision as of 14:13, 12 September 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
somite2.49e-1783
paraxial mesoderm2.49e-1783
presomitic mesoderm2.49e-1783
presumptive segmental plate2.49e-1783
trunk paraxial mesoderm2.49e-1783
presumptive paraxial mesoderm2.49e-1783
organism subdivision2.67e-17365
skeletal muscle tissue4.97e-1661
striated muscle tissue4.97e-1661
myotome4.97e-1661
multi-tissue structure5.29e-16347
dermomyotome9.11e-1670
muscle tissue1.06e-1563
musculature1.06e-1563
musculature of body1.06e-1563
trunk mesenchyme1.67e-15143
multilaminar epithelium3.05e-1382
epithelium1.75e-12309
cell layer2.03e-12312
trunk2.82e-12216
artery5.55e-1242
arterial blood vessel5.55e-1242
arterial system5.55e-1242
systemic artery5.43e-1033
systemic arterial system5.43e-1033
vasculature6.80e-1079
vascular system6.80e-1079
anatomical cluster7.54e-10286
mesenchyme9.17e-10238
entire embryonic mesenchyme9.17e-10238
unilaminar epithelium1.19e-09138
splanchnic layer of lateral plate mesoderm1.93e-0984
multi-cellular organism1.95e-09659
epithelial tube2.32e-09118
blood vessel1.22e-0860
epithelial tube open at both ends1.22e-0860
blood vasculature1.22e-0860
vascular cord1.22e-0860
cardiovascular system2.24e-07110
circulatory system2.48e-07113
anatomical system3.24e-07625
anatomical group3.66e-07626
tube4.28e-07194
vessel5.98e-0769


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.