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Coexpression cluster:C950: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 21:01, 8 August 2012


Full id: C950_liposarcoma_extraskeletal_Fibroblast_Smooth_Preadipocyte_neuroblastoma_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:14440817..14440832,+p24@TRIO
Hg19::chr5:14440848..14440864,+p22@TRIO
Hg19::chr5:14440872..14440890,+p13@TRIO
Hg19::chr5:14440903..14440920,+p6@TRIO
Hg19::chr5:14440934..14440949,+p10@TRIO
Hg19::chr5:14441117..14441141,+p5@TRIO
Hg19::chr5:14441157..14441216,+p3@TRIO
Hg19::chr5:14441222..14441241,+p4@TRIO
Hg19::chr5:14441335..14441346,+p18@TRIO


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
organism subdivision8.98e-27365
dermomyotome3.26e-2370
somite3.02e-2283
paraxial mesoderm3.02e-2283
presomitic mesoderm3.02e-2283
presumptive segmental plate3.02e-2283
trunk paraxial mesoderm3.02e-2283
presumptive paraxial mesoderm3.02e-2283
cell layer1.10e-21312
epithelium2.81e-20309
muscle tissue1.94e-1963
musculature1.94e-1963
musculature of body1.94e-1963
skeletal muscle tissue2.63e-1961
striated muscle tissue2.63e-1961
myotome2.63e-1961
multi-tissue structure2.14e-18347
regional part of nervous system2.89e-1794
nervous system2.89e-1794
multilaminar epithelium4.04e-1782
central nervous system1.86e-1682
neural plate2.20e-1686
presumptive neural plate2.20e-1686
neurectoderm5.64e-1690
brain1.05e-1569
future brain1.05e-1569
regional part of brain2.07e-1559
anterior region of body7.45e-15129
craniocervical region7.45e-15129
head1.61e-14123
multi-cellular organism1.75e-14659
adult organism2.02e-14115
ectoderm-derived structure3.11e-14169
ectoderm3.91e-14173
presumptive ectoderm3.91e-14173
neural tube1.04e-1357
neural rod1.04e-1357
future spinal cord1.04e-1357
neural keel1.04e-1357
tube1.68e-13194
anatomical cluster1.84e-13286
pre-chordal neural plate2.40e-1361
trunk mesenchyme1.61e-12143
anatomical system6.84e-12625
anterior neural tube8.68e-1242
regional part of forebrain8.83e-1241
forebrain8.83e-1241
future forebrain8.83e-1241
anatomical group1.10e-11626
telencephalon4.27e-1134
anatomical conduit5.68e-11241
cerebral hemisphere7.89e-1132
regional part of telencephalon1.02e-1033
vasculature1.21e-1079
vascular system1.21e-1079
gray matter1.46e-1034
brain grey matter1.46e-1034
regional part of cerebral cortex3.01e-1022
splanchnic layer of lateral plate mesoderm3.26e-1084
tissue3.74e-10787
cerebral cortex5.63e-1025
pallium5.63e-1025
neocortex9.78e-1020
embryo1.33e-09612
embryonic structure1.46e-09605
developing anatomical structure1.46e-09605
germ layer2.69e-09604
embryonic tissue2.69e-09604
presumptive structure2.69e-09604
epiblast (generic)2.69e-09604
artery7.28e-0942
arterial blood vessel7.28e-0942
arterial system7.28e-0942
systemic artery1.45e-0833
systemic arterial system1.45e-0833
circulatory system1.70e-08113
cardiovascular system2.56e-08110
blood vessel8.80e-0860
epithelial tube open at both ends8.80e-0860
blood vasculature8.80e-0860
vascular cord8.80e-0860
trunk2.32e-07216
integument2.44e-0745
integumental system2.44e-0745


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)

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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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