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Coexpression cluster:C3706: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279236986307183!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325053098650114!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321895156920866!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461883804448639!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156650192206468!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766963349035712!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024815130206037!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615557694777458!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329084417485298!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014007528692075
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279236986307183!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325053098650114!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321895156920866!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461883804448639!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156650192206468!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766963349035712!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024815130206037!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615557694777458!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329084417485298!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014007528692075
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}}
}}

Revision as of 16:18, 26 November 2012


Full id: C3706_temporal_duodenum_occipital_Neural_mucinous_parietal_Neurons



Phase1 CAGE Peaks

Hg19::chr18:12657866..12657958,-p2@SPIRE1
Hg19::chr18:12657964..12657987,-p3@SPIRE1
Hg19::chr18:12657988..12658128,-p1@SPIRE1


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
neural tube3.74e-2656
neural rod3.74e-2656
future spinal cord3.74e-2656
neural keel3.74e-2656
central nervous system3.86e-2581
nervous system5.77e-2589
regional part of nervous system1.68e-2453
regional part of brain1.68e-2453
brain3.47e-2268
future brain3.47e-2268
regional part of forebrain1.50e-2141
forebrain1.50e-2141
anterior neural tube1.50e-2141
future forebrain1.50e-2141
multi-cellular organism2.38e-21656
anatomical system3.01e-21624
anatomical group4.08e-21625
neural plate1.76e-2082
presumptive neural plate1.76e-2082
brain grey matter5.72e-1934
gray matter5.72e-1934
telencephalon6.04e-1934
structure with developmental contribution from neural crest2.92e-18132
neurectoderm3.34e-1886
organ4.60e-18503
regional part of telencephalon9.32e-1832
cerebral hemisphere9.77e-1832
embryo4.91e-17592
developing anatomical structure1.69e-16581
ecto-epithelium1.82e-16104
pre-chordal neural plate2.56e-1661
adult organism6.84e-16114
ectoderm-derived structure2.33e-15171
ectoderm2.33e-15171
presumptive ectoderm2.33e-15171
embryonic structure1.59e-14564
germ layer2.41e-14560
germ layer / neural crest2.41e-14560
embryonic tissue2.41e-14560
presumptive structure2.41e-14560
germ layer / neural crest derived structure2.41e-14560
epiblast (generic)2.41e-14560
cerebral cortex4.70e-1425
pallium4.70e-1425
regional part of cerebral cortex7.19e-1422
neocortex9.46e-1320
tube1.61e-12192
anatomical cluster3.37e-12373
anatomical conduit3.66e-12240
organ system subdivision1.36e-10223
epithelium3.25e-08306
cell layer3.85e-08309
multi-tissue structure2.13e-07342


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
CTCF#1066435.360256373075030.0064925092527670.0279236986307183
E2F1#186934.907389214879320.008460985347239390.0325053098650114
E2F6#187635.017155731697390.00791769806886330.0321895156920866
ELF1#199734.258097958807540.01295179875054610.0461883804448639
JUND#372736.994663941871030.002921845042734990.0156650192206468
REST#597839.650028716128020.001112636247114590.00766963349035712
TFAP2A#7020316.5186343730450.0002218033880766340.0024815130206037
TFAP2C#7022310.80922860986020.0007916746575753130.00615557694777458
YY1#752834.911170749853860.008441455341808260.0329084417485298
ZBTB7A#5134137.35190930787590.002516255860282270.014007528692075



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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