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Coexpression cluster:C995

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Full id: C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b



Phase1 CAGE Peaks

  Short description
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 clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
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 clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Uber Anatomy
Ontology termp-valuen
blood1.14e-1715
haemolymphatic fluid1.14e-1715
organism substance1.14e-1715
spleen1.68e-113
gastrointestinal system mesentery1.68e-113
stomach region1.68e-113
mesentery1.68e-113
gastrointestinal system serosa1.68e-113
mesentery of stomach1.68e-113
gut mesentery1.68e-113
dorsal mesentery1.68e-113
dorsal mesogastrium1.68e-113
peritoneal cavity1.68e-113
spleen primordium1.68e-113
adult organism1.28e-10114
major salivary gland2.61e-082
hemopoietic organ2.64e-087
immune organ2.64e-087
Disease
Ontology termp-valuen
lymphoma3.62e-1310


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
EBF1#187955.566541779105630.0007445813282558610.00586406223827116
NFE2#4778219.30106516290730.004458388692795240.0210988108517306
NFKB1#479074.802055496169614.48248622098168e-050.000794006747681658
PAX5#507975.83586983978061.18321811145587e-050.000299283401168177
POU2F2#545277.967858550524711.39153702916505e-065.41470699660838e-05
SPI1#668844.102161754261360.01027800662400760.0381933724890493
SRF#672246.89858913108390.001522071904568780.0097017801428904
TAF1#687262.507284714308970.01111734475613860.0408846920309293
TBP#690873.243424351209340.0006354223620492050.005213928038188
ZEB1#693536.333162006578950.009275222683824870.0350417805627255



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.