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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2038_adipose_heart_mature_lung_breast_Lymphatic_vagina
|full_id=C2038_adipose_heart_mature_lung_breast_Lymphatic_vagina
|id=C2038
|id=C2038

Revision as of 14:42, 12 September 2012


Full id: C2038_adipose_heart_mature_lung_breast_Lymphatic_vagina



Phase1 CAGE Peaks

Hg19::chr10:116444107..116444116,-p33@ABLIM1
Hg19::chr10:116444143..116444213,-p6@ABLIM1
Hg19::chr10:116444216..116444241,-p10@ABLIM1
Hg19::chr5:66311078..66311108,+p@chr5:66311078..66311108
+


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 organism1.71e-38115
anatomical cluster3.18e-31286
anatomical conduit8.21e-31241
epithelium3.75e-25309
tube3.28e-24194
anatomical system3.64e-24625
cell layer4.21e-24312
multi-cellular organism4.36e-24659
anatomical group6.90e-24626
multi-tissue structure8.07e-18347
embryonic structure1.06e-16605
developing anatomical structure1.06e-16605
embryo2.56e-16612
germ layer2.63e-16604
embryonic tissue2.63e-16604
presumptive structure2.63e-16604
epiblast (generic)2.63e-16604
neural plate7.20e-1686
presumptive neural plate7.20e-1686
organism subdivision1.26e-15365
neural tube1.28e-1557
neural rod1.28e-1557
future spinal cord1.28e-1557
neural keel1.28e-1557
regional part of brain6.52e-1559
neurectoderm9.04e-1590
organ1.66e-14511
brain2.20e-1369
future brain2.20e-1369
vasculature2.34e-1379
vascular system2.34e-1379
anterior region of body2.93e-13129
craniocervical region2.93e-13129
endothelium8.30e-1318
blood vessel endothelium8.30e-1318
cardiovascular system endothelium8.30e-1318
head9.23e-13123
splanchnic layer of lateral plate mesoderm5.42e-1284
central nervous system6.95e-1282
vessel1.38e-1169
epithelial tube1.70e-11118
regional part of nervous system3.43e-1194
nervous system3.43e-1194
anterior neural tube4.59e-1142
circulatory system5.31e-11113
ectoderm-derived structure1.53e-10169
regional part of forebrain1.82e-1041
forebrain1.82e-1041
future forebrain1.82e-1041
organ part2.47e-10219
ectoderm4.72e-10173
presumptive ectoderm4.72e-10173
cardiovascular system9.77e-10110
pre-chordal neural plate1.03e-0961
blood vessel2.18e-0960
epithelial tube open at both ends2.18e-0960
blood vasculature2.18e-0960
vascular cord2.18e-0960
simple squamous epithelium2.27e-0922
squamous epithelium3.31e-0925
compound organ1.07e-0869
gray matter1.24e-0834
brain grey matter1.24e-0834
telencephalon1.51e-0834
regional part of telencephalon3.01e-0833
unilaminar epithelium6.83e-08138
cerebral hemisphere7.28e-0832
endothelial tube2.05e-079
arterial system endothelium2.05e-079
endothelium of artery2.05e-079
regional part of cerebral cortex2.64e-0722
primary circulatory organ5.57e-0727


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
CEBPB#105135.978360719368610.007153832484726970.0297108645513342
FOS#235336.74846648167080.005032452776317940.0234510233582844
MAFF#23764342.23651736745892.20786227449124e-050.000483714973957606
MAFK#7975320.32554985337240.0001953213688931110.00235013461357461
NR3C1#2908311.22976749837980.001131672068063850.00775122633240562
STAT1#6772315.52994062289940.000434088655175550.00404711525244414
STAT3#6774410.51946499715428.16377768286615e-050.00122820048605713
TFAP2C#702238.106921457395170.002947011739866440.0157128323003835



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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