Personal tools

Coexpression cluster:C1051

From FANTOM5_SSTAR

Revision as of 13:28, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1051_umbilical_tenocyte_Mesenchymal_mesenchymal_Olfactory_Adipocyte_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr17:48261691..48261699,-p@chr17:48261691..48261699
-
Hg19::chr17:48262330..48262350,+p5@AB032018
Hg19::chr2:189859488..189859525,-p@chr2:189859488..189859525
-
Hg19::chr2:189859546..189859562,-p@chr2:189859546..189859562
-
Hg19::chr2:189861210..189861232,-p@chr2:189861210..189861232
-
Hg19::chr2:189861914..189861937,-p@chr2:189861914..189861937
-
Hg19::chr2:189867707..189867750,-p@chr2:189867707..189867750
-
Hg19::chr2:189871161..189871181,-p@chr2:189871161..189871181
-


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
dermomyotome7.22e-2070
somite1.11e-1983
paraxial mesoderm1.11e-1983
presomitic mesoderm1.11e-1983
presumptive segmental plate1.11e-1983
trunk paraxial mesoderm1.11e-1983
presumptive paraxial mesoderm1.11e-1983
muscle tissue5.92e-1963
musculature5.92e-1963
musculature of body5.92e-1963
skeletal muscle tissue9.74e-1961
striated muscle tissue9.74e-1961
myotome9.74e-1961
multilaminar epithelium3.57e-1682
trunk mesenchyme2.51e-13143
splanchnic layer of lateral plate mesoderm7.60e-1184
trunk9.59e-09216
adipose tissue1.54e-0814
heart1.96e-0824
primitive heart tube1.96e-0824
primary heart field1.96e-0824
anterior lateral plate mesoderm1.96e-0824
heart tube1.96e-0824
heart primordium1.96e-0824
cardiac mesoderm1.96e-0824
cardiogenic plate1.96e-0824
heart rudiment1.96e-0824
unilaminar epithelium2.39e-08138
mesenchyme2.91e-08238
entire embryonic mesenchyme2.91e-08238
multi-tissue structure3.91e-08347
primary circulatory organ5.10e-0827
extraembryonic structure1.30e-0724
organ component layer3.61e-0757
organism subdivision9.51e-07365


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.