Personal tools

Coexpression cluster:C995

From FANTOM5_SSTAR

Revision as of 15:00, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b



Phase1 CAGE Peaks

Hg19::chr11:60233507..60233518,+p3@MS4A1
Hg19::chr1:207103754..207103765,-p12@PIGR
Hg19::chr3:105975093..105975118,+p@chr3:105975093..105975118
+
Hg19::chr3:186739681..186739693,+p7@ST6GAL1
Hg19::chr3:186739710..186739719,+p14@ST6GAL1
Hg19::chr3:186739722..186739731,+p13@ST6GAL1
Hg19::chr8:110535027..110535055,+p2@PKHD1L1
Hg19::chr8:110535062..110535067,+p4@PKHD1L1


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:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.0268432668755767
GO:0009311oligosaccharide metabolic process0.0408673311549087
GO:0008373sialyltransferase activity0.0408673311549087
GO:0006955immune response0.0408673311549087
GO:0005887integral to plasma membrane0.0408673311549087
GO:0031226intrinsic to plasma membrane0.0408673311549087
GO:0002376immune system process0.0408673311549087
GO:0009306protein secretion0.0408673311549087
GO:0030173integral to Golgi membrane0.0408673311549087
GO:0042113B cell activation0.0408673311549087
GO:0031228intrinsic to Golgi membrane0.0418550013339888
GO:0006959humoral immune response0.0418550013339888
GO:0016021integral to membrane0.0422278845053486
GO:0031224intrinsic to membrane0.0422278845053486
GO:0044425membrane part0.048599195518169
GO:0031301integral to organelle membrane0.048599195518169
GO:0044459plasma membrane part0.048599195518169
GO:0031300intrinsic to organelle membrane0.048599195518169
GO:0008565protein transporter activity0.048599195518169
GO:0046649lymphocyte activation0.048599195518169
GO:0006486protein amino acid glycosylation0.048599195518169
GO:0005057receptor signaling protein activity0.048599195518169
GO:0043413biopolymer glycosylation0.048599195518169
GO:0045321leukocyte activation0.048599195518169
GO:0009101glycoprotein biosynthetic process0.048599195518169



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 organism2.19e-49115
neural tube3.05e-1257
neural rod3.05e-1257
future spinal cord3.05e-1257
neural keel3.05e-1257
regional part of forebrain3.25e-1141
forebrain3.25e-1141
future forebrain3.25e-1141
anterior neural tube9.36e-1142
blood9.89e-1015
haemolymphatic fluid9.89e-1015
organism substance9.89e-1015
regional part of brain1.09e-0959
telencephalon2.49e-0934
gray matter5.43e-0934
brain grey matter5.43e-0934
regional part of telencephalon8.88e-0933
cerebral hemisphere3.54e-0832
brain4.41e-0869
future brain4.41e-0869
central nervous system4.47e-0882
nucleus of brain1.90e-079
neural nucleus1.90e-079
neural plate3.18e-0786
presumptive neural plate3.18e-0786


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:C995&oldid=1708473"