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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4785_Retinal_hepatoma_small_Lens_prostate_neuroepithelioma_pancreas
|full_id=C4785_Retinal_hepatoma_small_Lens_prostate_neuroepithelioma_pancreas
|id=C4785
|id=C4785

Revision as of 17:55, 12 September 2012


Full id: C4785_Retinal_hepatoma_small_Lens_prostate_neuroepithelioma_pancreas



Phase1 CAGE Peaks

Hg19::chr8:99076762..99076782,+p3@C8orf47
Hg19::chr8:99076787..99076809,+p1@C8orf47
Hg19::chr8:99076820..99076848,+p2@C8orf47


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 organism7.50e-17115
multi-tissue structure2.55e-14347
neural plate3.82e-1486
presumptive neural plate3.82e-1486
neurectoderm9.52e-1490
pre-chordal neural plate1.37e-1261
organ part3.29e-12219
organism subdivision4.30e-12365
organ1.03e-11511
regional part of forebrain2.67e-1141
forebrain2.67e-1141
future forebrain2.67e-1141
anterior region of body4.02e-11129
craniocervical region4.02e-11129
head4.61e-11123
regional part of brain6.60e-1159
regional part of nervous system9.13e-1194
nervous system9.13e-1194
neural tube9.28e-1157
neural rod9.28e-1157
future spinal cord9.28e-1157
neural keel9.28e-1157
cerebral hemisphere1.06e-1032
anterior neural tube1.06e-1042
gray matter1.84e-1034
brain grey matter1.84e-1034
cell layer2.17e-10312
brain2.53e-1069
future brain2.53e-1069
ectoderm-derived structure2.92e-10169
ectoderm3.61e-10173
presumptive ectoderm3.61e-10173
epithelium5.27e-10309
telencephalon5.81e-1034
central nervous system6.30e-1082
regional part of telencephalon1.04e-0933
anatomical conduit5.60e-09241
neocortex6.95e-0920
intermediate mesoderm9.41e-0937
urinary system structure1.81e-0844
regional part of cerebral cortex2.34e-0822
abdomen element4.28e-0855
abdominal segment element4.28e-0855
renal system5.26e-0845
abdominal segment of trunk1.35e-0761
abdomen1.35e-0761
cerebral cortex1.64e-0725
pallium1.64e-0725
pigment epithelium of eye2.03e-0711
tube2.57e-07194
male organism3.39e-0722
male reproductive system3.39e-0722
anatomical cluster4.94e-07286
cavitated compound organ5.40e-0732
kidney8.11e-0727
kidney mesenchyme8.11e-0727
kidney rudiment8.11e-0727
kidney field8.11e-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
CTCF#1066435.360256373075030.0064925092527670.0281591019040587
ZNF263#1012738.221841637010680.001799043925565870.01102060816131



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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