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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2752_pineal_duodenum_occipital_Fibroblast_lung_amygdala_insula
|full_id=C2752_pineal_duodenum_occipital_Fibroblast_lung_amygdala_insula
|id=C2752
|id=C2752

Revision as of 15:31, 12 September 2012


Full id: C2752_pineal_duodenum_occipital_Fibroblast_lung_amygdala_insula



Phase1 CAGE Peaks

Hg19::chr3:74663774..74663788,-p@chr3:74663774..74663788
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Hg19::chr3:74663803..74663825,-p@chr3:74663803..74663825
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Hg19::chr3:74663830..74663873,-p@chr3:74663830..74663873
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Hg19::chr3:74663957..74663973,-p@chr3:74663957..74663973
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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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.34e-29115
neural tube1.86e-2757
neural rod1.86e-2757
future spinal cord1.86e-2757
neural keel1.86e-2757
organism subdivision6.73e-26365
neural plate1.02e-2586
presumptive neural plate1.02e-2586
regional part of brain1.80e-2459
central nervous system3.90e-2482
neurectoderm5.27e-2490
regional part of forebrain6.46e-2441
forebrain6.46e-2441
future forebrain6.46e-2441
anterior neural tube6.57e-2442
ectoderm-derived structure1.38e-22169
regional part of nervous system5.02e-2294
nervous system5.02e-2294
ectoderm1.15e-21173
presumptive ectoderm1.15e-21173
brain4.52e-2169
future brain4.52e-2169
pre-chordal neural plate1.88e-2061
telencephalon3.17e-2034
epithelium3.18e-20309
gray matter4.48e-2034
brain grey matter4.48e-2034
regional part of telencephalon1.46e-1933
cerebral hemisphere1.48e-1932
cell layer2.30e-19312
tube2.17e-18194
head6.00e-18123
anatomical conduit8.63e-18241
anterior region of body1.06e-17129
craniocervical region1.06e-17129
regional part of cerebral cortex1.39e-1622
cerebral cortex1.58e-1625
pallium1.58e-1625
anatomical cluster3.54e-16286
multi-cellular organism8.71e-16659
neocortex3.24e-1520
anatomical system2.02e-14625
anatomical group3.20e-14626
multi-tissue structure8.96e-14347
systemic artery3.87e-1333
systemic arterial system3.87e-1333
artery2.02e-1242
arterial blood vessel2.02e-1242
arterial system2.02e-1242
organ part4.48e-09219
muscle tissue5.89e-0963
musculature5.89e-0963
musculature of body5.89e-0963
embryo6.15e-09612
tissue1.45e-08787
dermomyotome1.50e-0870
skeletal muscle tissue1.90e-0861
striated muscle tissue1.90e-0861
myotome1.90e-0861
organ2.44e-08511
somite2.69e-0883
paraxial mesoderm2.69e-0883
presomitic mesoderm2.69e-0883
presumptive segmental plate2.69e-0883
trunk paraxial mesoderm2.69e-0883
presumptive paraxial mesoderm2.69e-0883
embryonic structure2.73e-08605
developing anatomical structure2.73e-08605
splanchnic layer of lateral plate mesoderm5.06e-0884
germ layer5.09e-08604
embryonic tissue5.09e-08604
presumptive structure5.09e-08604
epiblast (generic)5.09e-08604
blood vessel9.98e-0860
epithelial tube open at both ends9.98e-0860
blood vasculature9.98e-0860
vascular cord9.98e-0860
aorta4.04e-0721
aortic system4.04e-0721
integument4.27e-0745
integumental system4.27e-0745
skin of body7.57e-0740


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
TAF1#687243.343046285745290.008005664898701650.0322919680347405



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.

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