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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1252_aorta_heart_Mesothelial_neuroblastoma_Endothelial_rhabdomyosarcoma_bladder
|full_id=C1252_aorta_heart_Mesothelial_neuroblastoma_Endothelial_rhabdomyosarcoma_bladder
|id=C1252
|id=C1252

Revision as of 13:45, 12 September 2012


Full id: C1252_aorta_heart_Mesothelial_neuroblastoma_Endothelial_rhabdomyosarcoma_bladder



Phase1 CAGE Peaks

Hg19::chr1:163114878..163114901,-p4@RGS5
Hg19::chr1:163115879..163115899,-p@chr1:163115879..163115899
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Hg19::chr1:163116681..163116700,-p@chr1:163116681..163116700
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Hg19::chr1:163116725..163116737,-p@chr1:163116725..163116737
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Hg19::chr1:163116929..163116952,-p@chr1:163116929..163116952
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Hg19::chr1:163116977..163117007,-p@chr1:163116977..163117007
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Hg19::chr1:163172695..163172712,-p1@RGS5


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 organism1.08e-44115
central nervous system3.69e-2782
regional part of nervous system4.35e-2794
nervous system4.35e-2794
neural plate2.35e-2686
presumptive neural plate2.35e-2686
anatomical cluster4.06e-26286
neural tube1.58e-2457
neural rod1.58e-2457
future spinal cord1.58e-2457
neural keel1.58e-2457
regional part of brain1.59e-2459
neurectoderm3.30e-2490
anatomical conduit3.88e-24241
tube4.45e-24194
brain1.10e-2369
future brain1.10e-2369
anterior neural tube3.65e-1942
cell layer5.98e-19312
regional part of forebrain1.38e-1841
forebrain1.38e-1841
future forebrain1.38e-1841
epithelium1.90e-18309
ectoderm-derived structure8.03e-17169
pre-chordal neural plate9.58e-1761
anterior region of body2.25e-16129
craniocervical region2.25e-16129
gray matter6.15e-1634
brain grey matter6.15e-1634
ectoderm7.64e-16173
presumptive ectoderm7.64e-16173
head7.89e-16123
telencephalon1.16e-1534
regional part of telencephalon3.13e-1533
multi-tissue structure6.52e-15347
cerebral hemisphere8.96e-1532
multi-cellular organism6.62e-14659
splanchnic layer of lateral plate mesoderm1.45e-1384
cerebral cortex9.68e-1225
pallium9.68e-1225
regional part of cerebral cortex1.05e-1122
anatomical system1.61e-11625
anatomical group2.49e-11626
organism subdivision2.85e-11365
embryo5.24e-11612
vasculature6.46e-1179
vascular system6.46e-1179
neocortex8.77e-1120
circulatory system2.34e-10113
blood vessel3.74e-1060
epithelial tube open at both ends3.74e-1060
blood vasculature3.74e-1060
vascular cord3.74e-1060
cardiovascular system1.94e-09110
embryonic structure2.44e-09605
developing anatomical structure2.44e-09605
vessel3.78e-0969
germ layer5.33e-09604
embryonic tissue5.33e-09604
presumptive structure5.33e-09604
epiblast (generic)5.33e-09604
primary circulatory organ1.58e-0827
organ2.67e-08511
epithelial tube4.27e-08118
heart2.60e-0724
primitive heart tube2.60e-0724
primary heart field2.60e-0724
anterior lateral plate mesoderm2.60e-0724
heart tube2.60e-0724
heart primordium2.60e-0724
cardiac mesoderm2.60e-0724
cardiogenic plate2.60e-0724
heart rudiment2.60e-0724
organ part5.20e-07219


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
EP300#203343.870823843556110.01142567586684480.0418638142666784
FOS#235345.141688747939660.004042095865678250.0193505890225326
GATA2#262459.103522666824285.45256227113712e-050.000923998297964124
JUN#372547.150188109906480.001171328177707770.00795916353621484



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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