Personal tools

Coexpression cluster:C1995

From FANTOM5_SSTAR

Revision as of 14:38, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1995_CD8_Natural_Whole_Basophils_blood_NK_CD14



Phase1 CAGE Peaks

Hg19::chr7:38256596..38256627,+p@chr7:38256596..38256627
+
Hg19::chr8:1806917..1806924,+p9@ARHGEF10
Hg19::chr8:2066795..2066804,+p9@MYOM2
Hg19::chr8:2066860..2066887,+p4@MYOM2
Hg19::chr8:2066895..2066902,+p7@MYOM2


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

GO IDGO nameFDR corrected p-value
GO:0032982myosin filament0.0184451436946571
GO:0005863striated muscle thick filament0.0184451436946571
GO:0005859muscle myosin complex0.0184451436946571
GO:0016460myosin II complex0.0184451436946571
GO:0006941striated muscle contraction0.0184451436946571
GO:0008307structural constituent of muscle0.0184451436946571
GO:0030017sarcomere0.0184451436946571
GO:0030016myofibril0.0184451436946571
GO:0044449contractile fiber part0.0184451436946571
GO:0043292contractile fiber0.0184451436946571
GO:0016459myosin complex0.0280167630630111
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0296769554212099
GO:0035023regulation of Rho protein signal transduction0.0296769554212099
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0296769554212099
GO:0003012muscle system process0.0296769554212099
GO:0006936muscle contraction0.0296769554212099
GO:0007266Rho protein signal transduction0.0318138999383419
GO:0015629actin cytoskeleton0.046702118871827
GO:0005085guanyl-nucleotide exchange factor activity0.046702118871827



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
adult organism5.99e-27115
neocortex4.08e-1220
regional part of cerebral cortex7.32e-1222
gray matter5.75e-1134
brain grey matter5.75e-1134
blood8.42e-1115
haemolymphatic fluid8.42e-1115
organism substance8.42e-1115
cerebral cortex8.95e-1125
pallium8.95e-1125
telencephalon2.76e-1034
cerebral hemisphere2.97e-1032
regional part of telencephalon1.36e-0933
anterior neural tube1.34e-0842
regional part of forebrain4.85e-0841
forebrain4.85e-0841
future forebrain4.85e-0841
hematopoietic system2.66e-07102
blood island2.66e-07102
gyrus3.08e-076
neural tube3.29e-0757
neural rod3.29e-0757
future spinal cord3.29e-0757
neural keel3.29e-0757


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1995&oldid=2136621"