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Difference between revisions of "Coexpression cluster:C2623"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0002390!1.35e-08!102;UBERON:0003061!1.35e-08!102;UBERON:0002193!1.75e-07!112;UBERON:0001737!2.45e-07!9;UBERON:0001557!9.50e-07!19
 
|ontology_enrichment_uberon=UBERON:0002390!1.35e-08!102;UBERON:0003061!1.35e-08!102;UBERON:0002193!1.75e-07!112;UBERON:0001737!2.45e-07!9;UBERON:0001557!9.50e-07!19
 +
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127455769083494!BRCA1#672;4:20.1842306432238:6.02116732184487e-06:0.000179567302663094!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487274317684539!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106591979031795!GTF2F1#2962;3:9.55474565756824:0.00182036231930478:0.0109005687899703!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186277164599738!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283022942627933!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387012831734688!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.3406877844624e-05!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227654058932865!RDBP#7936;3:115.228802992519:1.09487348454017e-06:4.54842847461777e-05!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195847449290772!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796986906878892!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297671499924486!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584826116481854!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140368392479968!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162831089654078!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638148061506905
 
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}}
 
}}

Revision as of 05:01, 5 September 2012


Full id: C2623_pituitary_thyroid_neuroectodermal_leiomyoblastoma_large_small_Whole



Phase1 CAGE Peaks

Hg19::chr20:57463899..57463921,+p34@GNAS
Hg19::chr20:57464170..57464181,+p9@GNAS
Hg19::chr20:57464200..57464214,+p6@GNAS
Hg19::chr20:57464223..57464241,+p3@GNAS


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
hematopoietic system1.35e-08102
blood island1.35e-08102
hemolymphoid system1.75e-07112
larynx2.45e-079
upper respiratory tract9.50e-0719


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
ATF3#467422.46317452600873.92475754624726e-060.000127455769083494
BRCA1#672420.18423064322386.02116732184487e-060.000179567302663094
CCNT2#90534.752151182721970.01386206996689490.0487274317684539
E2F1#186944.907389214879320.001724022357361790.0106591979031795
GTF2F1#296239.554745657568240.001820362319304780.0109005687899703
HEY1#2346244.040111043105710.00375304636917980.0186277164599738
HMGN3#932436.133910792512940.006640696683324720.0283022942627933
JUND#372735.245997956403270.01043432751748420.0387012831734688
NANOG#79923429.24477848101271.36586687657858e-065.3406877844624e-05
POU2F2#545236.829593043306890.004860473775203740.0227654058932865
RDBP#79363115.2288029925191.09487348454017e-064.54842847461777e-05
REST#597837.237521537096020.004104697304192610.0195847449290772
SIN3A#2594245.408884726815140.001168172384885160.00796986906878892
SIX5#147912417.0867153554591.17257016123224e-050.000297671499924486
SRF#6722413.79717826216782.75840773062708e-050.000584826116481854
TAF7#687938.574802053692940.00250055433515240.0140368392479968
TCF12#693837.975848676639820.003090920396013070.0162831089654078
TFAP2A#7020312.38897577978370.000846941303588430.00638148061506905



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.