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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C332_Fibroblast_Smooth_Mesenchymal_mesenchymal_Chondrocyte_Skeletal_Pericytes
|full_id=C332_Fibroblast_Smooth_Mesenchymal_mesenchymal_Chondrocyte_Skeletal_Pericytes
|id=C332
|id=C332

Revision as of 16:14, 12 September 2012


Full id: C332_Fibroblast_Smooth_Mesenchymal_mesenchymal_Chondrocyte_Skeletal_Pericytes



Phase1 CAGE Peaks

Hg19::chr2:238233052..238233077,-p@chr2:238233052..238233077
-
Hg19::chr2:238233102..238233125,-p@chr2:238233102..238233125
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Hg19::chr2:238233169..238233193,-p@chr2:238233169..238233193
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Hg19::chr2:238233200..238233214,-p@chr2:238233200..238233214
-
Hg19::chr2:238233221..238233252,-p@chr2:238233221..238233252
-
Hg19::chr2:238233270..238233287,-p@chr2:238233270..238233287
-
Hg19::chr2:238233328..238233343,-p@chr2:238233328..238233343
-
Hg19::chr2:238233367..238233381,-p@chr2:238233367..238233381
-
Hg19::chr2:238233399..238233412,-p@chr2:238233399..238233412
-
Hg19::chr2:238243426..238243476,-p5@COL6A3
Hg19::chr2:238245036..238245087,-p@chr2:238245036..238245087
-
Hg19::chr2:238245089..238245122,-p@chr2:238245089..238245122
-
Hg19::chr2:238245140..238245185,-p@chr2:238245140..238245185
-
Hg19::chr2:238247690..238247710,-p@chr2:238247690..238247710
-
Hg19::chr2:238249113..238249142,-p11@COL6A3
Hg19::chr2:238267705..238267736,-p@chr2:238267705..238267736
-
Hg19::chr2:238267881..238267893,-p@chr2:238267881..238267893
-
Hg19::chr2:238268028..238268038,-p25@COL6A3
Hg19::chr2:238269787..238269823,-p@chr2:238269787..238269823
-
Hg19::chr2:238270402..238270421,-p7@COL6A3
Hg19::chr2:238271931..238271942,-p@chr2:238271931..238271942
-
Hg19::chr2:238271947..238271972,-p@chr2:238271947..238271972
-
Hg19::chr2:238275490..238275526,-p@chr2:238275490..238275526
-
Hg19::chr2:238277500..238277511,-p17@COL6A3
Hg19::chr2:238277567..238277581,-p9@COL6A3
Hg19::chr2:238289803..238289845,-p@chr2:238289803..238289845
-
Hg19::chr2:238289886..238289905,-p@chr2:238289886..238289905
-
Hg19::chr2:238289901..238289937,+p@chr2:238289901..238289937
+
Hg19::chr2:238305397..238305434,-p10@COL6A3
Hg19::chr2:238322770..238322791,-p2@COL6A3
Hg19::chr2:238322800..238322824,-p1@COL6A3
Hg19::chr2:238322913..238322923,-p12@COL6A3
Hg19::chr2:238322924..238322940,-p6@COL6A3
Hg19::chr2:238322983..238323006,-p4@COL6A3
Hg19::chr2:238323007..238323038,-p3@COL6A3


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
somite9.41e-2383
paraxial mesoderm9.41e-2383
presomitic mesoderm9.41e-2383
presumptive segmental plate9.41e-2383
trunk paraxial mesoderm9.41e-2383
presumptive paraxial mesoderm9.41e-2383
dermomyotome5.08e-2070
trunk mesenchyme2.96e-18143
muscle tissue2.80e-1763
musculature2.80e-1763
musculature of body2.80e-1763
skeletal muscle tissue5.46e-1761
striated muscle tissue5.46e-1761
myotome5.46e-1761
multilaminar epithelium1.47e-1682
organism subdivision8.80e-16365
trunk2.62e-11216
multi-tissue structure3.56e-11347
surface structure6.43e-1195
integument4.65e-1045
integumental system4.65e-1045
multi-cellular organism2.32e-09659
skin of body4.56e-0840
mesenchyme5.06e-08238
entire embryonic mesenchyme5.06e-08238
adipose tissue2.12e-0714
primary circulatory organ2.44e-0727
tissue3.31e-07787
heart4.62e-0724
primitive heart tube4.62e-0724
primary heart field4.62e-0724
anterior lateral plate mesoderm4.62e-0724
heart tube4.62e-0724
heart primordium4.62e-0724
cardiac mesoderm4.62e-0724
cardiogenic plate4.62e-0724
heart rudiment4.62e-0724
splanchnic layer of lateral plate mesoderm6.61e-0784


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

No analysis results for this cluster

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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