Personal tools

Coexpression cluster:C3968

From FANTOM5_SSTAR

Revision as of 16:28, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3968_Fibroblast_Adipocyte_Hair_Pericytes_Preadipocyte_Skeletal_Prostate



Phase1 CAGE Peaks

Hg19::chr1:31882992..31883005,+p14@SERINC2
Hg19::chr1:31883012..31883032,+p6@SERINC2
Hg19::chr1:31883057..31883076,+p7@SERINC2


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
surface structure4.71e-1599
periodontium1.81e-106
dentition1.81e-106
skull6.65e-097
gingiva4.73e-088
integument9.39e-0846
integumental system9.39e-0846
skeletal muscle tissue1.16e-0762
striated muscle tissue1.16e-0762
myotome1.16e-0762
muscle tissue2.72e-0764
musculature2.72e-0764
musculature of body2.72e-0764
somite3.97e-0771
presomitic mesoderm3.97e-0771
presumptive segmental plate3.97e-0771
dermomyotome3.97e-0771
trunk paraxial mesoderm3.97e-0771
paraxial mesoderm5.73e-0772
presumptive paraxial mesoderm5.73e-0772
omentum7.66e-076
peritoneum7.66e-076
abdominal cavity7.66e-076
visceral peritoneum7.66e-076
dense mesenchyme tissue8.18e-0773
organism subdivision8.27e-07264
mouth8.30e-0729
stomodeum8.30e-0729


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA1#2623313.56030814380040.0004009615963782630.00388172304079991



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.