Personal tools

Coexpression cluster:C3002

From FANTOM5_SSTAR

Revision as of 14:31, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3002_Mast_CD34_acute_CD4_Melanocyte_chronic_CD133



Phase1 CAGE Peaks

Hg19::chr10:17496557..17496568,-p3@ST8SIA6
Hg19::chr10:17496582..17496601,-p1@ST8SIA6
Hg19::chr10:17496614..17496625,-p5@ST8SIA6


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
mature alpha-beta T cell9.00e-0918
alpha-beta T cell9.00e-0918
immature T cell9.00e-0918
mature T cell9.00e-0918
immature alpha-beta T cell9.00e-0918
T cell3.80e-0825
pro-T cell3.80e-0825
CD8-positive, alpha-beta T cell4.57e-0711
Uber Anatomy
Ontology termp-valuen
adult organism9.61e-30115
neural tube1.45e-1457
neural rod1.45e-1457
future spinal cord1.45e-1457
neural keel1.45e-1457
regional part of brain7.74e-1359
central nervous system5.73e-1282
neural plate8.96e-1286
presumptive neural plate8.96e-1286
brain1.19e-1169
future brain1.19e-1169
regional part of nervous system1.83e-1094
nervous system1.83e-1094
neurectoderm2.83e-1090
anterior neural tube6.05e-1042
regional part of forebrain1.72e-0941
forebrain1.72e-0941
future forebrain1.72e-0941
regional part of cerebral cortex5.68e-0822
telencephalon5.81e-0834
gray matter6.04e-0834
brain grey matter6.04e-0834
pre-chordal neural plate1.19e-0761
regional part of telencephalon1.44e-0733
neocortex2.34e-0720
cerebral hemisphere2.93e-0732
anterior region of body5.12e-07129
craniocervical region5.12e-07129
blood6.21e-0715
haemolymphatic fluid6.21e-0715
organism substance6.21e-0715
cerebral cortex8.88e-0725
pallium8.88e-0725
Disease
Ontology termp-valuen
myeloid leukemia2.76e-0931
leukemia5.27e-0839


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.