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Coexpression cluster:C4045: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279859331317732!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173129615717522
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279859331317732!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173129615717522
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}}
}}

Revision as of 16:31, 26 November 2012


Full id: C4045_neuroblastoma_cord_dura_salivary_seminal_medulloblastoma_small



Phase1 CAGE Peaks

Hg19::chr20:45523452..45523459,+p5@EYA2
Hg19::chr20:45523463..45523535,+p1@EYA2
Hg19::chr20:45523539..45523563,+p3@EYA2


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 organism1.10e-31114
neural plate3.02e-1482
presumptive neural plate3.02e-1482
organ system subdivision3.29e-14223
central nervous system4.82e-1481
neural tube5.26e-1456
neural rod5.26e-1456
future spinal cord5.26e-1456
neural keel5.26e-1456
brain2.73e-1368
future brain2.73e-1368
neurectoderm9.87e-1386
regional part of nervous system2.63e-1253
regional part of brain2.63e-1253
nervous system8.96e-1289
ectoderm-derived structure6.54e-11171
ectoderm6.54e-11171
presumptive ectoderm6.54e-11171
pre-chordal neural plate1.02e-1061
regional part of forebrain1.41e-1041
forebrain1.41e-1041
anterior neural tube1.41e-1041
future forebrain1.41e-1041
brain grey matter1.67e-1034
gray matter1.67e-1034
telencephalon2.96e-1034
cerebral hemisphere1.40e-0932
regional part of telencephalon1.45e-0932
ecto-epithelium3.05e-09104
structure with developmental contribution from neural crest4.09e-09132
regional part of cerebral cortex3.66e-0822
neocortex3.09e-0720
anatomical cluster4.47e-07373


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
CTCF#1066435.360256373075030.0064925092527670.0279859331317732
PAX5#507936.669565531177830.003370290999677260.0173129615717522



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.