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Coexpression cluster:C1362: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466002587505026!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255587898292926
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466002587505026!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255587898292926
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}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1362_Preadipocyte_Adipocyte_Fibroblast_Mesenchymal_mesenchymal_Myoblast_Smooth



Phase1 CAGE Peaks

Hg19::chr12:54402694..54402705,+p5@HOXC8
Hg19::chr12:54402729..54402743,+p3@HOXC8
Hg19::chr12:54402745..54402788,+p1@HOXC8
Hg19::chr12:54402790..54402805,+p2@HOXC8
Hg19::chr12:54410639..54410659,+p2@HOXC4
p2@HOXC5
p2@HOXC6
Hg19::chr12:54410664..54410684,+p1@HOXC4
p1@HOXC5
p1@HOXC6


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


GO IDGO nameFDR corrected p-value
GO:0043565sequence-specific DNA binding0.0289572869453141
GO:0003700transcription factor activity0.0355826006899583
GO:0007275multicellular organismal development0.0355826006899583
GO:0032502developmental process0.0355826006899583
GO:0006355regulation of transcription, DNA-dependent0.0355826006899583
GO:0006351transcription, DNA-dependent0.0355826006899583
GO:0032774RNA biosynthetic process0.0355826006899583
GO:0003677DNA binding0.0355826006899583
GO:0045449regulation of transcription0.0355826006899583
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0355826006899583
GO:0030182neuron differentiation0.0355826006899583
GO:0006350transcription0.0355826006899583
GO:0032501multicellular organismal process0.0355826006899583
GO:0010468regulation of gene expression0.0355826006899583
GO:0031323regulation of cellular metabolic process0.0355826006899583
GO:0048699generation of neurons0.0355826006899583
GO:0019222regulation of metabolic process0.0355826006899583
GO:0016070RNA metabolic process0.0355826006899583
GO:0022008neurogenesis0.0355826006899583



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
fat cell6.85e-1215
skin fibroblast1.53e-1123
preadipocyte6.06e-1112
fibroblast9.20e-1176
mesenchymal stem cell of adipose1.99e-078
non-terminally differentiated cell3.08e-07106
Uber Anatomy
Ontology termp-valuen
integument3.96e-1346
integumental system3.96e-1346
adipose tissue3.39e-1114
skin of body2.48e-1041
trunk8.21e-09199
mesenchyme4.21e-08160
entire embryonic mesenchyme4.21e-08160
body cavity or lining3.58e-0749
articulation6.83e-078
skeletal joint6.83e-078
articular system6.83e-078


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)

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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
CTCF#1066443.573504248716680.01316635007238510.0466002587505026
SUZ12#23512216.70526030368760.005660234682079570.0255587898292926



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.