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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3591_acute_pituitary_smallcell_leukemia_chronic_temporal_testis
|full_id=C3591_acute_pituitary_smallcell_leukemia_chronic_temporal_testis
|id=C3591
|id=C3591

Revision as of 16:32, 12 September 2012


Full id: C3591_acute_pituitary_smallcell_leukemia_chronic_temporal_testis



Phase1 CAGE Peaks

Hg19::chr16:81684951..81684960,+p@chr16:81684951..81684960
+
Hg19::chr16:81684964..81684969,+p@chr16:81684964..81684969
+
Hg19::chr16:81684985..81685002,+p@chr16:81684985..81685002
+


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 organism1.59e-32115
neurectoderm1.39e-1490
neural plate1.80e-1386
presumptive neural plate1.80e-1386
central nervous system3.08e-1382
neural tube3.61e-1357
neural rod3.61e-1357
future spinal cord3.61e-1357
neural keel3.61e-1357
regional part of nervous system3.30e-1294
nervous system3.30e-1294
ectoderm5.11e-11173
presumptive ectoderm5.11e-11173
regional part of brain1.92e-1059
ectoderm-derived structure3.88e-10169
anterior neural tube2.14e-0942
pre-chordal neural plate3.76e-0961
brain5.07e-0969
future brain5.07e-0969
regional part of forebrain5.73e-0941
forebrain5.73e-0941
future forebrain5.73e-0941
anterior region of body4.31e-07129
craniocervical region4.31e-07129


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
E2F6#187635.017155731697390.00791769806886330.0321557189537258
EGR1#195834.988179094810140.008056488137383440.0320086569247228
HMGN3#932438.178547723350590.001827766942164210.0108596058523546
ZBTB7A#5134137.35190930787590.002516255860282270.0139963381866223



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.