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Coexpression cluster:C2803: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:37, 8 August 2012


Full id: C2803_granulosa_Fibroblast_Smooth_cholangiocellular_Mesenchymal_hepatic_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:136312914..136312928,-p@chr5:136312914..136312928
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Hg19::chr5:136313104..136313119,-p@chr5:136313104..136313119
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Hg19::chr5:136313255..136313279,-p@chr5:136313255..136313279
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Hg19::chr5:136834982..136835025,-p1@SPOCK1


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
epithelium1.36e-25309
tube2.07e-25194
cell layer6.44e-25312
anatomical cluster8.55e-25286
anatomical conduit1.30e-24241
organism subdivision2.25e-23365
neural tube7.51e-1957
neural rod7.51e-1957
future spinal cord7.51e-1957
neural keel7.51e-1957
multi-cellular organism1.17e-18659
neural plate1.54e-1786
presumptive neural plate1.54e-1786
splanchnic layer of lateral plate mesoderm8.92e-1784
regional part of brain1.86e-1659
neurectoderm8.56e-1690
regional part of nervous system1.14e-1594
nervous system1.14e-1594
anatomical system2.33e-15625
central nervous system2.37e-1582
anatomical group4.70e-15626
regional part of forebrain6.20e-1541
forebrain6.20e-1541
future forebrain6.20e-1541
anterior neural tube6.81e-1542
blood vessel9.11e-1560
epithelial tube open at both ends9.11e-1560
blood vasculature9.11e-1560
vascular cord9.11e-1560
artery1.02e-1442
arterial blood vessel1.02e-1442
arterial system1.02e-1442
brain1.59e-1469
future brain1.59e-1469
multi-tissue structure5.49e-14347
vasculature1.85e-1379
vascular system1.85e-1379
pre-chordal neural plate2.78e-1361
vessel3.17e-1369
gray matter1.11e-1234
brain grey matter1.11e-1234
telencephalon1.16e-1234
regional part of telencephalon2.36e-1233
systemic artery5.91e-1233
systemic arterial system5.91e-1233
cerebral hemisphere9.50e-1232
head1.11e-11123
ectoderm-derived structure1.43e-11169
embryo3.20e-11612
embryonic structure4.53e-11605
developing anatomical structure4.53e-11605
anterior region of body5.08e-11129
craniocervical region5.08e-11129
germ layer7.48e-11604
embryonic tissue7.48e-11604
presumptive structure7.48e-11604
epiblast (generic)7.48e-11604
ectoderm1.04e-10173
presumptive ectoderm1.04e-10173
epithelial tube2.35e-10118
cardiovascular system3.90e-10110
circulatory system3.94e-10113
cerebral cortex4.98e-1025
pallium4.98e-1025
skeletal muscle tissue6.39e-1061
striated muscle tissue6.39e-1061
myotome6.39e-1061
adult organism8.63e-10115
regional part of cerebral cortex9.89e-1022
muscle tissue1.12e-0963
musculature1.12e-0963
musculature of body1.12e-0963
multilaminar epithelium5.50e-0982
neocortex6.28e-0920
organ part8.69e-09219
dermomyotome1.78e-0870
somite2.73e-0883
paraxial mesoderm2.73e-0883
presomitic mesoderm2.73e-0883
presumptive segmental plate2.73e-0883
trunk paraxial mesoderm2.73e-0883
presumptive paraxial mesoderm2.73e-0883
unilaminar epithelium2.84e-08138
aorta1.95e-0721
aortic system1.95e-0721


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.

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