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Coexpression cluster:C3573: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:16, 8 August 2012


Full id: C3573_liver_Bronchial_Mesenchymal_Fibroblast_Tracheal_Keratinocyte_Mammary



Phase1 CAGE Peaks

Hg19::chr16:56643233..56643256,+p@chr16:56643233..56643256
+
Hg19::chr16:56643260..56643307,+p@chr16:56643260..56643307
+
Hg19::chr16:56643282..56643333,-p@chr16:56643282..56643333
-


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
cell layer4.99e-27312
epithelium6.61e-26309
trunk mesenchyme2.04e-21143
multilaminar epithelium1.37e-2082
anatomical cluster4.07e-20286
organism subdivision7.33e-20365
trunk1.85e-19216
epithelial tube2.10e-19118
multi-tissue structure2.48e-19347
somite4.74e-1983
paraxial mesoderm4.74e-1983
presomitic mesoderm4.74e-1983
presumptive segmental plate4.74e-1983
trunk paraxial mesoderm4.74e-1983
presumptive paraxial mesoderm4.74e-1983
vasculature5.89e-1879
vascular system5.89e-1879
unilaminar epithelium1.26e-17138
dermomyotome1.58e-1770
anatomical conduit5.70e-17241
vessel1.66e-1569
mesenchyme5.83e-15238
entire embryonic mesenchyme5.83e-15238
skeletal muscle tissue2.08e-1461
striated muscle tissue2.08e-1461
myotome2.08e-1461
tube3.27e-14194
blood vessel8.28e-1460
epithelial tube open at both ends8.28e-1460
blood vasculature8.28e-1460
vascular cord8.28e-1460
muscle tissue1.05e-1363
musculature1.05e-1363
musculature of body1.05e-1363
artery2.04e-1342
arterial blood vessel2.04e-1342
arterial system2.04e-1342
anatomical system9.52e-12625
circulatory system1.03e-11113
splanchnic layer of lateral plate mesoderm1.26e-1184
cardiovascular system1.40e-11110
anatomical group1.66e-11626
germ layer8.88e-11604
embryonic tissue8.88e-11604
presumptive structure8.88e-11604
epiblast (generic)8.88e-11604
embryonic structure1.16e-10605
developing anatomical structure1.16e-10605
multi-cellular organism1.66e-10659
systemic artery1.80e-1033
systemic arterial system1.80e-1033
embryo2.46e-09612
nephron epithelium1.53e-0716
nephron1.53e-0716
uriniferous tubule1.53e-0716
metanephric mesenchyme1.53e-0716
nephrogenic mesenchyme1.53e-0716
excretory tube3.73e-0717
mesonephric epithelium3.73e-0717
mesonephric tubule3.73e-0717
nephric duct3.73e-0717
kidney epithelium3.73e-0717
renal duct3.73e-0717
mesonephric duct3.73e-0717
pronephric duct3.73e-0717
simple squamous epithelium4.33e-0722
squamous epithelium7.34e-0725
organ part8.51e-07219


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.