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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3244_heart_lung_giant_Endothelial_Renal_Placental_skeletal
|full_id=C3244_heart_lung_giant_Endothelial_Renal_Placental_skeletal
|id=C3244
|id=C3244

Revision as of 16:08, 12 September 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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.32e-42115
anatomical conduit1.83e-17241
anatomical cluster1.45e-14286
tube7.19e-13194
neural tube2.81e-1257
neural rod2.81e-1257
future spinal cord2.81e-1257
neural keel2.81e-1257
anterior neural tube1.12e-1042
neural plate3.90e-1086
presumptive neural plate3.90e-1086
regional part of forebrain4.94e-1041
forebrain4.94e-1041
future forebrain4.94e-1041
regional part of brain1.39e-0959
neurectoderm6.40e-0990
cell layer7.03e-09312
epithelium8.73e-09309
organ part9.54e-09219
gray matter1.08e-0834
brain grey matter1.08e-0834
brain1.11e-0869
future brain1.11e-0869
endothelium1.30e-0818
blood vessel endothelium1.30e-0818
cardiovascular system endothelium1.30e-0818
compound organ3.39e-0869
telencephalon3.77e-0834
regional part of telencephalon7.27e-0833
cerebral hemisphere1.67e-0732
central nervous system2.39e-0782
anatomical system5.45e-07625
pre-chordal neural plate6.19e-0761
anatomical group7.04e-07626
anterior region of body7.24e-07129
craniocervical region7.24e-07129
simple squamous epithelium9.55e-0722


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
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.

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