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Coexpression cluster:C2936: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346536551401938!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487504032485616!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0173084930363305!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820676133870618!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441163101042059!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192165352290058!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283173167119774!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466475222141833!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601766426905632!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00766111915017637!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483433265079303!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107275930603204!ZBTB33#10009;3:23.7485437724859:0.000122945190881838:0.00165659563804777!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342646386540668!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00977197096797509
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346536551401938!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487504032485616!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0173084930363305!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820676133870618!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441163101042059!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192165352290058!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283173167119774!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466475222141833!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601766426905632!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00766111915017637!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483433265079303!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107275930603204!ZBTB33#10009;3:23.7485437724859:0.000122945190881838:0.00165659563804777!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342646386540668!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00977197096797509
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}}
}}

Revision as of 15:49, 26 November 2012


Full id: C2936_CD14_parotid_salivary_submaxillary_corpus_Mallassezderived_substantia



Phase1 CAGE Peaks

Hg19::chr9:115913230..115913266,+p2@SLC31A2
Hg19::chr9:115913271..115913298,+p1@SLC31A2
Hg19::chr9:115913314..115913325,+p3@SLC31A2
Hg19::chr9:115915412..115915416,+p@chr9:115915412..115915416
+


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 system2.91e-2598
blood island2.91e-2598
hemolymphoid system2.29e-24108
bone marrow5.94e-2376
immune system2.48e-2093
adult organism5.52e-19114
bone element1.03e-1882
skeletal element2.04e-1890
skeletal system8.87e-17100
embryonic structure2.82e-09564
anatomical system1.06e-08624
musculoskeletal system1.13e-08167
germ layer1.23e-08560
germ layer / neural crest1.23e-08560
embryonic tissue1.23e-08560
presumptive structure1.23e-08560
germ layer / neural crest derived structure1.23e-08560
epiblast (generic)1.23e-08560
anatomical group1.65e-08625
organ1.97e-08503
neural tube6.51e-0856
neural rod6.51e-0856
future spinal cord6.51e-0856
neural keel6.51e-0856
developing anatomical structure7.16e-08581
regional part of nervous system4.47e-0753
regional part of brain4.47e-0753
multi-cellular organism9.77e-07656


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#467316.84738089450660.0003409986823655640.00346536551401938
CCNT2#90534.752151182721970.01386206996689490.0487504032485616
CHD2#110637.758017125587640.003351522464536340.0173084930363305
CTCF#1066445.360256373075030.001211145381643620.00820676133870618
CTCFL#140690314.80985576923080.0004996291767563340.00441163101042059
ETS1#211337.296570691651750.00400857377511390.0192165352290058
HMGN3#932436.133910792512940.006640696683324720.0283173167119774
MAX#414934.839416631755340.01315737137836840.0466475222141833
SIX5#147912312.81503651659420.0007664471136930380.00601766426905632
SMC3#9126311.28369963369960.001115802366868050.00766111915017637
USF1#739134.771124457905970.01370465887188020.0483433265079303
USF2#739239.74414803880220.001718341848410070.0107275930603204
ZBTB33#10009323.74854377248590.0001229451908818380.00165659563804777
ZBTB7A#5134135.513931980906920.009038352821081090.0342646386540668
ZNF143#7702310.12565741417090.001534861610688180.00977197096797509



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.