Personal tools

Coexpression cluster:C2895

From FANTOM5_SSTAR

Revision as of 18:42, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2895_immature_Mallassezderived_mesenchymal_CD14_Fibroblast_migratory_Endothelial



Phase1 CAGE Peaks

Hg19::chr7:39663146..39663225,+p1@RALA
Hg19::chr7:39663255..39663276,+p3@RALA
Hg19::chr7:39663286..39663317,+p2@RALA
Hg19::chr7:39663534..39663558,+p5@RALA


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>disease_data<br>


Cell Type
Ontology termp-valuen
mesodermal cell7.98e-19119
somatic cell3.67e-16591
animal cell7.23e-16679
eukaryotic cell7.23e-16679
non-terminally differentiated cell6.53e-14180
endothelial cell of vascular tree1.44e-1324
endothelial cell2.00e-1235
somatic stem cell3.31e-12436
multi fate stem cell3.66e-12430
stem cell1.56e-11444
muscle precursor cell7.28e-1157
myoblast7.28e-1157
multi-potent skeletal muscle stem cell7.28e-1157
vascular associated smooth muscle cell9.59e-1132
blood vessel endothelial cell1.08e-1018
embryonic blood vessel endothelial progenitor cell1.08e-1018
embryonic cell2.11e-10248
fibroblast2.22e-1075
muscle cell3.28e-1054
native cell3.35e-10722
lining cell8.60e-1057
barrier cell8.60e-1057
meso-epithelial cell1.51e-0944
smooth muscle cell2.22e-0942
smooth muscle myoblast2.22e-0942
CD14-positive, CD16-negative classical monocyte3.82e-0942
electrically responsive cell4.98e-0960
electrically active cell4.98e-0960
contractile cell4.00e-0859
classical monocyte9.68e-0845
cardiocyte8.01e-0716
macrophage dendritic cell progenitor8.11e-0765
Uber Anatomy
Ontology termp-valuen
vessel9.44e-2169
blood vessel2.92e-1960
epithelial tube open at both ends2.92e-1960
blood vasculature2.92e-1960
vascular cord2.92e-1960
vasculature3.70e-1979
vascular system3.70e-1979
splanchnic layer of lateral plate mesoderm7.01e-1884
artery3.00e-1742
arterial blood vessel3.00e-1742
arterial system3.00e-1742
systemic artery1.86e-1333
systemic arterial system1.86e-1333
cardiovascular system1.09e-12110
musculoskeletal system3.43e-12167
circulatory system2.72e-11113
somite5.22e-1183
paraxial mesoderm5.22e-1183
presomitic mesoderm5.22e-1183
presumptive segmental plate5.22e-1183
trunk paraxial mesoderm5.22e-1183
presumptive paraxial mesoderm5.22e-1183
endothelium1.08e-1018
blood vessel endothelium1.08e-1018
cardiovascular system endothelium1.08e-1018
aorta3.96e-1021
aortic system3.96e-1021
epithelial tube2.51e-09118
dermomyotome2.72e-0970
mesoderm3.70e-09448
mesoderm-derived structure3.70e-09448
presumptive mesoderm3.70e-09448
simple squamous epithelium5.79e-0922
multilaminar epithelium7.10e-0982
skeletal muscle tissue7.26e-0961
striated muscle tissue7.26e-0961
myotome7.26e-0961
muscle tissue1.58e-0863
musculature1.58e-0863
musculature of body1.58e-0863
anatomical system4.43e-08625
lateral plate mesoderm6.09e-08216
anatomical group6.19e-08626
squamous epithelium9.35e-0825
unilaminar epithelium1.77e-07138
multi-cellular organism7.82e-07659
Disease
Ontology termp-valuen
ovarian cancer1.02e-0714


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.