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Coexpression cluster:C2841: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998951587109522!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186534245348484!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486287038459691!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889554133769812!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172769801228443!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327187349970482!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114799755579509!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230755865138731!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508900379531383!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682575462120163!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107030725029349
|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998951587109522!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186534245348484!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486287038459691!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889554133769812!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172769801228443!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327187349970482!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114799755579509!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230755865138731!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508900379531383!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682575462120163!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107030725029349
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}}
}}

Revision as of 15:45, 26 November 2012


Full id: C2841_sacrococcigeal_CD14_Smooth_colon_Prostate_anaplastic_tridermal



Phase1 CAGE Peaks

Hg19::chr6:123110302..123110313,+p4@SMPDL3A
Hg19::chr6:123110370..123110382,+p2@SMPDL3A
Hg19::chr6:123110389..123110441,+p1@SMPDL3A
Hg19::chr6:123110465..123110480,+p3@SMPDL3A


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
multi-cellular organism9.25e-24656
organ4.92e-22503
anatomical system1.03e-18624
anatomical group2.43e-18625
germ layer1.46e-17560
germ layer / neural crest1.46e-17560
embryonic tissue1.46e-17560
presumptive structure1.46e-17560
germ layer / neural crest derived structure1.46e-17560
epiblast (generic)1.46e-17560
embryonic structure1.52e-17564
developing anatomical structure1.84e-16581
embryo2.30e-15592
bone marrow2.45e-1276
bone element5.05e-1182
skeletal element1.08e-1090
skeletal system2.94e-10100
musculoskeletal system6.55e-10167
adult organism1.08e-09114
immune system1.42e-0993
hematopoietic system3.05e-0998
blood island3.05e-0998
organ system subdivision1.65e-08223
hemolymphoid system5.25e-08108
gastrointestinal system6.35e-0725
intestine9.41e-0717


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#187645.017155731697390.00157802193473060.00998951587109522
HEY1#2346244.040111043105710.00375304636917980.0186534245348484
MAX#414946.452555509007120.0005767613195645490.00486287038459691
MYC#460945.22228187160940.001344309395272740.00889554133769812
RAD21#588537.766275421592250.0033411193858720.0172769801228443
TFAP2A#7020416.5186343730451.34240829060362e-050.000327187349970482
TFAP2C#7022410.80922860986027.32289634782688e-050.00114799755579509
TRIM28#10155418.59052504526258.36730015875654e-060.000230755865138731
USF1#739146.361499277207960.0006105011399140830.00508900379531383
USF2#7392412.99219738506963.50833029870167e-050.000682575462120163
YY1#752844.911170749853860.00171871838055440.0107030725029349



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.