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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1044_Renal_amniotic_Mammary_chorionic_bile_prostate_Amniotic
|full_id=C1044_Renal_amniotic_Mammary_chorionic_bile_prostate_Amniotic
|id=C1044
|id=C1044

Revision as of 13:28, 12 September 2012


Full id: C1044_Renal_amniotic_Mammary_chorionic_bile_prostate_Amniotic



Phase1 CAGE Peaks

Hg19::chr16:61687533..61687551,-p@chr16:61687533..61687551
-
Hg19::chr16:62055187..62055188,+p@chr16:62055187..62055188
+
Hg19::chr3:123667850..123667851,+p@chr3:123667850..123667851
+
Hg19::chr6:30890348..30890372,+p5@VARS2
Hg19::chr6:30890373..30890381,+p9@VARS2
Hg19::chr6:30890456..30890482,+p11@VARS2
Hg19::chr6:30890599..30890626,+p4@VARS2
Hg19::chr8:6614884..6614885,+p@chr8:6614884..6614885
+


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
renal tubule2.69e-1912
nephron tubule2.69e-1912
nephron tubule epithelium2.69e-1912
nephron epithelium7.14e-1716
nephron7.14e-1716
uriniferous tubule7.14e-1716
metanephric mesenchyme7.14e-1716
nephrogenic mesenchyme7.14e-1716
extraembryonic membrane6.95e-1614
membranous layer6.95e-1614
excretory tube1.04e-1517
mesonephric epithelium1.04e-1517
mesonephric tubule1.04e-1517
nephric duct1.04e-1517
kidney epithelium1.04e-1517
renal duct1.04e-1517
mesonephric duct1.04e-1517
pronephric duct1.04e-1517
mesonephros1.12e-1418
pronephros1.12e-1418
nephrogenic cord1.12e-1418
pronephric mesoderm1.12e-1418
rostral part of nephrogenic cord1.12e-1418
presumptive pronephric mesoderm1.12e-1418
kidney3.41e-1427
kidney mesenchyme3.41e-1427
kidney rudiment3.41e-1427
kidney field3.41e-1427
duct4.27e-1326
urinary system structure5.43e-1344
urogenital ridge6.30e-1320
intermediate mesoderm7.63e-1337
renal system1.36e-1245
intraembryonic coelom3.53e-1221
cavitated compound organ2.14e-1132
cortex of kidney3.10e-1113
renal parenchyma3.10e-1113
cortex7.41e-1116
extraembryonic structure7.02e-1024
organ part1.14e-09219
compound organ3.13e-0969
amnion4.63e-097
renal cortex tubule9.53e-093
region of nephron tubule9.53e-093
proximal tubule9.53e-093
chorion1.85e-087
parenchyma3.39e-0817
somatic layer of lateral plate mesoderm7.42e-088
abdomen element6.56e-0755
abdominal segment element6.56e-0755


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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