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Coexpression cluster:C2538

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Full id: C2538_parietal_occipital_uterus_cervix_rectum_brain_duodenum



Phase1 CAGE Peaks

Hg19::chr1:164557736..164557744,+p@chr1:164557736..164557744
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Hg19::chr1:164568324..164568328,+p@chr1:164568324..164568328
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Hg19::chr1:164600535..164600539,+p@chr1:164600535..164600539
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Hg19::chr1:164693945..164693950,+p@chr1:164693945..164693950
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.23e-28114
central nervous system3.94e-2881
nervous system3.07e-2789
organ system subdivision3.17e-26223
brain6.81e-2568
future brain6.81e-2568
neural tube5.60e-2456
neural rod5.60e-2456
future spinal cord5.60e-2456
neural keel5.60e-2456
regional part of nervous system1.24e-2253
regional part of brain1.24e-2253
neurectoderm1.07e-2186
regional part of forebrain1.16e-2041
forebrain1.16e-2041
anterior neural tube1.16e-2041
future forebrain1.16e-2041
ectoderm-derived structure2.62e-20171
ectoderm2.62e-20171
presumptive ectoderm2.62e-20171
neural plate2.64e-2082
presumptive neural plate2.64e-2082
telencephalon7.67e-1834
brain grey matter2.13e-1734
gray matter2.13e-1734
regional part of telencephalon8.13e-1732
cerebral hemisphere9.27e-1732
anatomical cluster2.04e-16373
pre-chordal neural plate1.34e-1561
cerebral cortex3.34e-1425
pallium3.34e-1425
multi-tissue structure1.02e-13342
structure with developmental contribution from neural crest2.76e-13132
ecto-epithelium3.22e-13104
regional part of cerebral cortex1.30e-1222
organ6.19e-12503
neocortex1.68e-1120
multi-cellular organism1.15e-10656
organ part8.14e-10218
anatomical conduit9.84e-09240
intestine5.22e-0817
germ layer9.84e-08560
germ layer / neural crest9.84e-08560
embryonic tissue9.84e-08560
presumptive structure9.84e-08560
germ layer / neural crest derived structure9.84e-08560
epiblast (generic)9.84e-08560
embryonic structure1.30e-07564
epithelium2.19e-07306
anatomical group2.24e-07625
anatomical system3.39e-07624
cell layer3.68e-07309
embryo3.89e-07592
digestive system9.71e-07145
digestive tract9.71e-07145
primitive gut9.71e-07145


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
GATA3#2625213.6182581786030.00769665208093340.0316942925116554



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.