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Coexpression cluster:C3244: Difference between revisions

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|tf_chipseq_enrich=NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308096208043495!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189669104312754
|tf_chipseq_enrich=NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308096208043495!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189669104312754
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3244_heart_lung_giant_Endothelial_Renal_Placental_skeletal



Phase1 CAGE Peaks

Hg19::chr12:120687725..120687742,-p28@PXN
Hg19::chr12:120687764..120687787,-p19@PXN
Hg19::chr12:120687798..120687841,-p11@PXN


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 organism1.30e-48114
neural tube4.69e-1356
neural rod4.69e-1356
future spinal cord4.69e-1356
neural keel4.69e-1356
regional part of nervous system2.95e-1253
regional part of brain2.95e-1253
anatomical conduit2.86e-11240
regional part of forebrain6.05e-1141
forebrain6.05e-1141
anterior neural tube6.05e-1141
future forebrain6.05e-1141
brain grey matter9.56e-1134
gray matter9.56e-1134
brain2.33e-1068
future brain2.33e-1068
neural plate7.22e-1082
presumptive neural plate7.22e-1082
central nervous system2.17e-0981
telencephalon2.27e-0934
regional part of telencephalon2.98e-0932
cerebral hemisphere3.04e-0932
neurectoderm6.08e-0986
organ part9.97e-09218
anatomical cluster1.24e-08373
tube1.69e-08192
structure with developmental contribution from neural crest1.69e-08132
nervous system1.61e-0789
compound organ2.41e-0768
basal ganglion2.58e-079
nuclear complex of neuraxis2.58e-079
aggregate regional part of brain2.58e-079
collection of basal ganglia2.58e-079
cerebral subcortex2.58e-079
regional part of cerebral cortex3.17e-0722
neural nucleus3.22e-079
nucleus of brain3.22e-079
neocortex6.37e-0720
chorion7.33e-077
multi-tissue structure8.10e-07342
ecto-epithelium9.86e-07104


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NR3C1#2908314.9730233311730.0002978331194675480.00308096208043495
USF1#739136.361499277207960.00388404057290560.0189669104312754



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.