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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte
|full_id=C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte
|id=C2053
|id=C2053

Revision as of 14:43, 12 September 2012


Full id: C2053_Fibroblast_tridermal_tenocyte_transitionalcell_normal_Pancreatic_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr10:28034739..28034756,-p1@MKX
Hg19::chr10:28035112..28035130,-p5@MKX
Hg19::chr10:28035133..28035148,-p3@MKX
Hg19::chr10:28035155..28035166,-p8@MKX


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
skin fibroblast2.13e-0923
fibroblast2.87e-0875
stromal cell9.43e-0727
Uber Anatomy
Ontology termp-valuen
adult organism2.67e-21115
neural tube9.50e-1757
neural rod9.50e-1757
future spinal cord9.50e-1757
neural keel9.50e-1757
head1.77e-15123
anterior region of body7.50e-15129
craniocervical region7.50e-15129
organism subdivision1.63e-14365
neurectoderm4.39e-1490
brain6.31e-1469
future brain6.31e-1469
neural plate8.89e-1486
presumptive neural plate8.89e-1486
regional part of brain1.18e-1359
central nervous system4.50e-1382
regional part of nervous system4.40e-1294
nervous system4.40e-1294
ectoderm1.13e-11173
presumptive ectoderm1.13e-11173
ectoderm-derived structure2.64e-11169
anterior neural tube3.94e-1142
gray matter9.41e-1134
brain grey matter9.41e-1134
regional part of forebrain1.13e-1041
forebrain1.13e-1041
future forebrain1.13e-1041
telencephalon1.58e-1034
organ3.00e-10511
regional part of telencephalon6.13e-1033
cerebral hemisphere7.46e-1032
multi-cellular organism1.12e-09659
neocortex8.75e-0920
surface structure9.82e-0995
multi-tissue structure1.49e-08347
regional part of cerebral cortex3.75e-0822
pre-chordal neural plate5.33e-0861
cerebral cortex3.21e-0725
pallium3.21e-0725
subdivision of skeletal system3.40e-0713
skeleton3.40e-0713
sclerotome3.40e-0713
larynx3.77e-079
posterior neural tube3.83e-0715
chordal neural plate3.83e-0715


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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