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Coexpression cluster:C4650: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281193984345083!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327583632504295!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187358634470938!MYC#4609;3:5.2222818716094:0.00702084375574015:0.02959636331002!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223349468990256!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110096301735717
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281193984345083!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327583632504295!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187358634470938!MYC#4609;3:5.2222818716094:0.00702084375574015:0.02959636331002!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223349468990256!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110096301735717
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}}
}}

Revision as of 16:52, 26 November 2012


Full id: C4650_neuroblastoma_neuroectodermal_mature_rhabdomyosarcoma_neuroepithelioma_small_acute



Phase1 CAGE Peaks

Hg19::chr7:128001737..128001749,-p2@PRRT4
Hg19::chr7:128001954..128001966,-p5@PRRT4
Hg19::chr7:128001971..128001994,-p1@PRRT4


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>disease_data<br>

Cell Type
Ontology termp-valuen
fat cell8.52e-0915
Uber Anatomy
Ontology termp-valuen
neurectoderm5.77e-2286
neural tube4.08e-2056
neural rod4.08e-2056
future spinal cord4.08e-2056
neural keel4.08e-2056
regional part of nervous system1.94e-1853
regional part of brain1.94e-1853
neural plate1.10e-1782
presumptive neural plate1.10e-1782
nervous system3.16e-1789
brain1.76e-1568
future brain1.76e-1568
central nervous system6.80e-1581
adult organism9.77e-15114
brain grey matter9.97e-1534
gray matter9.97e-1534
telencephalon1.38e-1434
cerebral hemisphere2.57e-1432
regional part of forebrain6.21e-1441
forebrain6.21e-1441
anterior neural tube6.21e-1441
future forebrain6.21e-1441
ecto-epithelium1.04e-13104
regional part of cerebral cortex1.12e-1322
neocortex1.85e-1320
ectoderm-derived structure4.88e-13171
ectoderm4.88e-13171
presumptive ectoderm4.88e-13171
regional part of telencephalon1.20e-1232
cerebral cortex1.30e-1125
pallium1.30e-1125
pre-chordal neural plate1.92e-1161
structure with developmental contribution from neural crest1.64e-08132
posterior neural tube1.54e-0715
chordal neural plate1.54e-0715
organ system subdivision4.06e-07223
sympathetic nervous system7.40e-075
autonomic nervous system7.40e-075
Disease
Ontology termp-valuen
neuroectodermal tumor4.42e-1210
germ cell and embryonal cancer5.26e-0822
germ cell cancer5.26e-0822


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#1066435.360256373075030.0064925092527670.0281193984345083
E2F1#186934.907389214879320.008460985347239390.0327583632504295
MAX#414936.452555509007120.003721913834265510.0187358634470938
MYC#460935.22228187160940.007020843755740150.02959636331002
SUZ12#23512350.11578091106297.93834897779404e-060.000223349468990256
ZNF263#1012738.221841637010680.001799043925565870.0110096301735717



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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