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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1083_lung_uterus_Endothelial_neuroectodermal_spleen_mesenchymal_occipital
|full_id=C1083_lung_uterus_Endothelial_neuroectodermal_spleen_mesenchymal_occipital
|id=C1083
|id=C1083

Revision as of 13:31, 12 September 2012


Full id: C1083_lung_uterus_Endothelial_neuroectodermal_spleen_mesenchymal_occipital



Phase1 CAGE Peaks

Hg19::chr4:16900023..16900034,-p7@LDB2
Hg19::chr4:16900184..16900195,-p6@LDB2
Hg19::chr4:16900198..16900214,-p2@LDB2
Hg19::chr4:16900219..16900230,-p5@LDB2
Hg19::chr4:16900242..16900317,-p1@LDB2
Hg19::chr4:16900320..16900332,-p8@LDB2
Hg19::chr4:16900395..16900407,-p3@LDB2
Hg19::chr4:16900410..16900427,-p4@LDB2


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 organism1.58e-31115
central nervous system1.66e-2082
regional part of nervous system6.63e-2094
nervous system6.63e-2094
anterior neural tube8.47e-2042
regional part of forebrain3.07e-1941
forebrain3.07e-1941
future forebrain3.07e-1941
neural tube3.69e-1957
neural rod3.69e-1957
future spinal cord3.69e-1957
neural keel3.69e-1957
cerebral hemisphere4.23e-1832
telencephalon5.51e-1834
regional part of brain6.69e-1859
regional part of telencephalon2.59e-1733
gray matter3.03e-1734
brain grey matter3.03e-1734
brain3.22e-1769
future brain3.22e-1769
anatomical conduit3.68e-17241
neurectoderm6.35e-1790
anatomical cluster6.72e-17286
tube3.48e-16194
cerebral cortex3.05e-1525
pallium3.05e-1525
regional part of cerebral cortex3.13e-1522
neural plate6.58e-1586
presumptive neural plate6.58e-1586
neocortex1.77e-1420
pre-chordal neural plate2.31e-1361
anterior region of body4.73e-12129
craniocervical region4.73e-12129
ectoderm7.35e-12173
presumptive ectoderm7.35e-12173
multi-cellular organism7.49e-12659
head1.48e-11123
cell layer2.12e-11312
epithelium3.10e-11309
splanchnic layer of lateral plate mesoderm1.25e-1084
ectoderm-derived structure2.00e-10169
vasculature2.57e-1079
vascular system2.57e-1079
circulatory system3.91e-10113
vessel5.31e-1069
organism subdivision6.95e-10365
cardiovascular system1.75e-09110
endothelium5.13e-0918
blood vessel endothelium5.13e-0918
cardiovascular system endothelium5.13e-0918
anatomical system2.10e-08625
blood vessel3.19e-0860
epithelial tube open at both ends3.19e-0860
blood vasculature3.19e-0860
vascular cord3.19e-0860
anatomical group3.22e-08626
simple squamous epithelium3.92e-0722
squamous epithelium6.11e-0725


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
SIN3A#2594285.408884726815141.36410592556506e-065.35384662758697e-05
TAF1#687283.343046285745296.40776711117462e-050.0010437005447972
USF1#739164.771124457905970.0003163361106003810.00324059117753735



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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