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Coexpression cluster:C4449: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115618304192946!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130213396690201!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280798067686655!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172191331920963!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327013858589421!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168118385983957!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435359827956413!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157401647711456!MAFF#23764;3:56.3153564899452:5.59409009993116e-06:0.00016919813957333!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000858830882926922!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066713769741867!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310338735909127!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155244256832308!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644753714635265!YY1#7528;3:4.91117074985386:0.00844145534180826:0.033073872840753!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109870971605271!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.38217595333689e-06
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115618304192946!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130213396690201!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280798067686655!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172191331920963!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327013858589421!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168118385983957!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435359827956413!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157401647711456!MAFF#23764;3:56.3153564899452:5.59409009993116e-06:0.00016919813957333!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000858830882926922!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066713769741867!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310338735909127!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155244256832308!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644753714635265!YY1#7528;3:4.91117074985386:0.00844145534180826:0.033073872840753!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109870971605271!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.38217595333689e-06
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4449_brain_temporal_occipital_cerebellum_duodenum_Neurons_parietal



Phase1 CAGE Peaks

Hg19::chr5:111092930..111092941,-p7@C5orf13
Hg19::chr5:111093123..111093136,-p6@C5orf13
Hg19::chr5:111093169..111093178,-p8@C5orf13


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
central nervous system2.29e-2281
nervous system2.82e-2289
brain2.71e-1968
future brain2.71e-1968
neural tube1.46e-1656
neural rod1.46e-1656
future spinal cord1.46e-1656
neural keel1.46e-1656
ectoderm-derived structure7.86e-16171
ectoderm7.86e-16171
presumptive ectoderm7.86e-16171
regional part of nervous system9.45e-1653
regional part of brain9.45e-1653
neural plate1.08e-1582
presumptive neural plate1.08e-1582
neurectoderm1.57e-1586
structure with developmental contribution from neural crest2.78e-13132
cerebral cortex1.34e-1225
pallium1.34e-1225
cerebral hemisphere2.13e-1232
telencephalon2.41e-1234
regional part of forebrain3.22e-1241
forebrain3.22e-1241
anterior neural tube3.22e-1241
future forebrain3.22e-1241
anatomical cluster3.54e-12373
tube4.31e-12192
regional part of cerebral cortex4.42e-1222
neocortex1.53e-1120
brain grey matter1.57e-1134
gray matter1.57e-1134
regional part of telencephalon2.07e-1132
pre-chordal neural plate4.16e-1161
ecto-epithelium4.62e-11104
organ system subdivision1.70e-10223
multi-cellular organism1.93e-10656
cell layer9.10e-10309
epithelium1.73e-09306
tissue1.03e-08773
anatomical conduit2.16e-08240
anatomical system5.81e-08624
anatomical group9.84e-08625
embryonic structure1.24e-07564
germ layer1.49e-07560
germ layer / neural crest1.49e-07560
embryonic tissue1.49e-07560
presumptive structure1.49e-07560
germ layer / neural crest derived structure1.49e-07560
epiblast (generic)1.49e-07560
developing anatomical structure3.44e-07581
multi-tissue structure4.03e-07342
embryo8.16e-07592


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
CEBPB#105137.971147625824820.001974187055288560.0115618304192946
CTBP2#1488362.71700033932814.049570681927e-060.000130213396690201
CTCF#1066435.360256373075030.0064925092527670.0280798067686655
CTCFL#140690319.74647435897440.0001298372005551160.00172191331920963
E2F1#186934.907389214879320.008460985347239390.0327013858589421
EP300#203336.77394172622320.003216880500103790.0168118385983957
GTF2F1#2962312.73966087675770.0004835525047438590.00435359827956413
JUND#372736.994663941871030.002921845042734990.0157401647711456
MAFF#23764356.31535648994525.59409009993116e-060.00016919813957333
MAFK#7975327.10073313782995.02195559325033e-050.000858830882926922
RAD21#5885310.35503389545630.0009004912073565420.0066713769741867
SMC3#9126315.04493284493280.0002935825420371870.00310338735909127
STAT1#6772320.70658749719920.0001125992441046670.00155244256832308
STAT3#6774310.51946499715420.0008589184530415310.00644753714635265
YY1#752834.911170749853860.008441455341808260.033073872840753
ZNF263#1012738.221841637010680.001799043925565870.0109870971605271
ZZZ3#260093239.4132124352337.25894005043406e-084.38217595333689e-06



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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