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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:02, 8 August 2012


Full id: C3271_gastric_giant_testicular_pancreatic_ductal_Fibroblast_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr12:26111751..26111762,+p7@RASSF8
Hg19::chr12:26111788..26111811,+p6@RASSF8
Hg19::chr12:26111823..26111862,+p2@RASSF8


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
non-terminally differentiated cell2.66e-23180
fibroblast4.84e-1675
skin fibroblast6.09e-0823
vascular associated smooth muscle cell1.52e-0732
mesodermal cell5.86e-07119
Uber Anatomy
Ontology termp-valuen
organism subdivision1.22e-14365
anatomical cluster2.67e-14286
multi-cellular organism5.70e-14659
anatomical group7.19e-13626
anatomical system1.03e-12625
multi-tissue structure3.63e-12347
vasculature3.91e-1079
vascular system3.91e-1079
artery5.51e-1042
arterial blood vessel5.51e-1042
arterial system5.51e-1042
cell layer6.08e-10312
splanchnic layer of lateral plate mesoderm6.20e-1084
epithelium8.92e-10309
somite1.14e-0983
paraxial mesoderm1.14e-0983
presomitic mesoderm1.14e-0983
presumptive segmental plate1.14e-0983
trunk paraxial mesoderm1.14e-0983
presumptive paraxial mesoderm1.14e-0983
anatomical conduit1.22e-09241
systemic artery1.50e-0933
systemic arterial system1.50e-0933
vessel4.31e-0969
blood vessel7.81e-0960
epithelial tube open at both ends7.81e-0960
blood vasculature7.81e-0960
vascular cord7.81e-0960
dermomyotome4.16e-0870
tube4.71e-08194
multilaminar epithelium1.90e-0782
organ2.08e-07511
trunk2.29e-07216
circulatory system2.67e-07113
cardiovascular system4.50e-07110
embryonic structure7.22e-07605
developing anatomical structure7.22e-07605
surface structure8.16e-0795
embryo9.40e-07612


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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