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Coexpression cluster:C2670

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Full id: C2670_uterus_lung_cervix_adipose_penis_ductus_seminal



Phase1 CAGE Peaks

Hg19::chr2:173686542..173686585,+p5@RAPGEF4
Hg19::chr5:38557323..38557328,-p12@LIFR
Hg19::chr5:38557343..38557361,-p4@LIFR
Hg19::chr5:38557372..38557385,-p5@LIFR


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:0004923leukemia inhibitory factor receptor activity0.0046508889673849
GO:0030552cAMP binding0.022470032592992
GO:0016208AMP binding0.022470032592992
GO:0005952cAMP-dependent protein kinase complex0.022470032592992
GO:0030551cyclic nucleotide binding0.022470032592992
GO:0008603cAMP-dependent protein kinase regulator activity0.022470032592992
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0457985933512357



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 organism6.05e-62115
anatomical conduit1.59e-28241
anatomical cluster2.07e-28286
neural tube1.29e-2657
neural rod1.29e-2657
future spinal cord1.29e-2657
neural keel1.29e-2657
tube2.41e-25194
regional part of brain4.72e-2359
anterior neural tube7.49e-2242
regional part of forebrain5.66e-2141
forebrain5.66e-2141
future forebrain5.66e-2141
central nervous system1.17e-2082
regional part of nervous system4.25e-1994
nervous system4.25e-1994
neural plate1.67e-1886
presumptive neural plate1.67e-1886
brain1.88e-1869
future brain1.88e-1869
gray matter9.48e-1834
brain grey matter9.48e-1834
neurectoderm1.36e-1790
telencephalon1.55e-1734
regional part of telencephalon6.60e-1733
cerebral hemisphere1.89e-1632
regional part of cerebral cortex6.37e-1422
cell layer1.24e-13312
epithelium2.08e-13309
neocortex9.83e-1320
cerebral cortex1.97e-1225
pallium1.97e-1225
pre-chordal neural plate2.93e-1261
endothelium4.98e-1118
blood vessel endothelium4.98e-1118
cardiovascular system endothelium4.98e-1118
multi-cellular organism3.27e-10659
anatomical group3.46e-10626
anterior region of body5.74e-10129
craniocervical region5.74e-10129
anatomical system6.94e-10625
multi-tissue structure1.95e-09347
head6.98e-09123
ectoderm-derived structure1.11e-08169
ectoderm1.97e-08173
presumptive ectoderm1.97e-08173
embryo4.30e-08612
simple squamous epithelium6.42e-0822
vessel9.13e-0869
embryonic structure2.19e-07605
developing anatomical structure2.19e-07605
splanchnic layer of lateral plate mesoderm2.22e-0784
brainstem3.66e-078
squamous epithelium4.44e-0725
germ layer4.74e-07604
embryonic tissue4.74e-07604
presumptive structure4.74e-07604
epiblast (generic)4.74e-07604
nucleus of brain6.76e-079
neural nucleus6.76e-079
circulatory system8.95e-07113


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
MXI1#460137.471178721569470.003741314738550960.0186385789915819
SMARCA4#65973117.5744274809161.03069197590886e-064.32828465106337e-05
SMARCB1#6598313.68953683586810.0006305783409379340.00518232383925219
SMARCC1#6599332.74751948972364.71941722862287e-050.000824922537138316
SMARCC2#6601370.61653082017324.74678670742709e-060.000147237795348078
ZNF263#1012736.166381227758010.006539814347975980.0279808140388473



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.