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Coexpression cluster:C2170: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2170_leiomyoma_Osteoblast_Monocytederived_Adipocyte_Smooth_tenocyte_Olfactory
|full_id=C2170_leiomyoma_Osteoblast_Monocytederived_Adipocyte_Smooth_tenocyte_Olfactory
|id=C2170
|id=C2170

Revision as of 14:51, 12 September 2012


Full id: C2170_leiomyoma_Osteoblast_Monocytederived_Adipocyte_Smooth_tenocyte_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:838495..838514,+p@chr11:838495..838514
+
Hg19::chr12:56120020..56120046,-p6@CD63
Hg19::chr12:56120969..56121013,-p8@CD63
Hg19::chr12:56121032..56121059,-p3@CD63


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
mesoderm2.54e-17448
mesoderm-derived structure2.54e-17448
presumptive mesoderm2.54e-17448
multi-cellular organism1.51e-15659
somite7.77e-1583
paraxial mesoderm7.77e-1583
presomitic mesoderm7.77e-1583
presumptive segmental plate7.77e-1583
trunk paraxial mesoderm7.77e-1583
presumptive paraxial mesoderm7.77e-1583
trunk mesenchyme4.72e-14143
dermomyotome1.55e-1370
anatomical system2.58e-12625
anatomical group3.65e-12626
multilaminar epithelium7.92e-1282
skeletal muscle tissue1.81e-1161
striated muscle tissue1.81e-1161
myotome1.81e-1161
muscle tissue3.94e-1163
musculature3.94e-1163
musculature of body3.94e-1163
trunk9.01e-11216
epithelial tube1.01e-10118
musculoskeletal system2.10e-10167
splanchnic layer of lateral plate mesoderm5.36e-1084
artery5.70e-1042
arterial blood vessel5.70e-1042
arterial system5.70e-1042
embryo1.22e-09612
vasculature2.93e-0979
vascular system2.93e-0979
blood vessel4.80e-0960
epithelial tube open at both ends4.80e-0960
blood vasculature4.80e-0960
vascular cord4.80e-0960
embryonic structure5.04e-09605
developing anatomical structure5.04e-09605
germ layer6.88e-09604
embryonic tissue6.88e-09604
presumptive structure6.88e-09604
epiblast (generic)6.88e-09604
vessel1.16e-0869
systemic artery3.18e-0833
systemic arterial system3.18e-0833
mesenchyme4.65e-08238
entire embryonic mesenchyme4.65e-08238
circulatory system6.72e-08113
unilaminar epithelium7.10e-08138
lateral plate mesoderm7.52e-08216
cardiovascular system1.90e-07110


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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