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Coexpression cluster:C2156: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296149165916713!BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226711750975375!BCLAF1#9774;3:16.2394857075914:0.00038025670676648:0.00376539586593196!CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487028434795308!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995151457287175!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240352684964235!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101285165469551!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418714109597739!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0191980298298308!FOSL1#8061;3:29.7851847872798:6.26173959487248e-05:0.00102487043025997!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378401301338831!GATA3#2625;2:13.618258178603:0.0076966520809334:0.03168804536132!HDAC2#3066;3:10.0617151774697:0.0015637275447474:0.00992127702119396!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390597605974938!HNF4G#3174;3:21.5650668948351:0.000163803242129261:0.00203538926885638!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386696970156678!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484526829584958!MEF2C#4208;2:20.655677246312:0.00340257057944504:0.0173550043341796!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186234769543646!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00885793873393624!NR2C2#7182;3:24.4609581789307:0.000112590606343803:0.00155499211001593!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.0044322751678705!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428216007613201!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765457720660357!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328022278051251!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404819939797118!STAT2#6773;2:32.6318855932203:0.00137958877512552:0.0089810429523988!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158574227613622
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}}
}}

Revision as of 15:20, 26 November 2012


Full id: C2156_Mesenchymal_Smooth_leiomyoma_Fibroblast_Myoblast_Preadipocyte_Hair



Phase1 CAGE Peaks

Hg19::chr11:65687158..65687216,+p4@DRAP1
Hg19::chr11:65687222..65687240,+p7@DRAP1
Hg19::chr11:65687243..65687276,+p8@DRAP1
Hg19::chr11:65687362..65687436,+p3@DRAP1


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
epithelial vesicle2.76e-2078
somite7.69e-2071
presomitic mesoderm7.69e-2071
presumptive segmental plate7.69e-2071
dermomyotome7.69e-2071
trunk paraxial mesoderm7.69e-2071
dense mesenchyme tissue9.82e-2073
multilaminar epithelium1.05e-1983
paraxial mesoderm1.85e-1972
presumptive paraxial mesoderm1.85e-1972
artery2.39e-1742
arterial blood vessel2.39e-1742
arterial system2.39e-1742
skeletal muscle tissue4.70e-1662
striated muscle tissue4.70e-1662
myotome4.70e-1662
systemic artery9.57e-1533
systemic arterial system9.57e-1533
muscle tissue1.51e-1464
musculature1.51e-1464
musculature of body1.51e-1464
surface structure6.16e-1499
vessel1.04e-1368
vasculature2.12e-1378
vascular system2.12e-1378
epithelial tube open at both ends3.16e-1359
blood vessel3.16e-1359
blood vasculature3.16e-1359
vascular cord3.16e-1359
unilaminar epithelium5.18e-12148
splanchnic layer of lateral plate mesoderm7.20e-1183
cardiovascular system2.15e-10109
trunk mesenchyme2.93e-10122
integument3.24e-1046
integumental system3.24e-1046
mesenchyme1.46e-09160
entire embryonic mesenchyme1.46e-09160
skin of body4.97e-0941
circulatory system5.20e-09112
organism subdivision5.35e-08264
aorta7.14e-0821
aortic system7.14e-0821
mesoderm2.70e-07315
mesoderm-derived structure2.70e-07315
presumptive mesoderm2.70e-07315
epithelial tube3.25e-07117
musculoskeletal system4.90e-07167
trunk6.75e-07199


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
BCL11A#53335214.18472755180350.007108328585298740.0296149165916713
BCL3#602217.27355140186920.004834494208076070.0226711750975375
BCLAF1#9774316.23948570759140.000380256706766480.00376539586593196
CCNT2#90534.752151182721970.01386206996689490.0487028434795308
E2F6#187645.017155731697390.00157802193473060.00995151457287175
EBF1#187936.679850134926750.005184294118278910.0240352684964235
EGR1#195844.988179094810140.001615011500076050.0101285165469551
EP300#203335.08045629466740.01144298405398240.0418714109597739
ETS1#211337.296570691651750.00400857377511390.0191980298298308
FOSL1#8061329.78518478727986.26173959487248e-050.00102487043025997
GABPB1#255335.300762877136630.01012678824234270.0378401301338831
GATA3#2625213.6182581786030.00769665208093340.03168804536132
HDAC2#3066310.06171517746970.00156372754474740.00992127702119396
HNF4A#3172211.56614518147680.01057585681762490.0390597605974938
HNF4G#3174321.56506689483510.0001638032421292610.00203538926885638
JUND#372735.245997956403270.01043432751748420.0386696970156678
MAX#414946.452555509007120.0005767613195645490.00484526829584958
MEF2C#4208220.6556772463120.003402570579445040.0173550043341796
MXI1#460137.471178721569470.003741314738550960.0186234769543646
MYC#460945.22228187160940.001344309395272740.00885793873393624
NR2C2#7182324.46095817893070.0001125906063438030.00155499211001593
PAX5#507946.669565531177830.0005052774169483260.0044322751678705
PBX3#5090210.95725634337210.01174530180688030.0428216007613201
SMC3#9126311.28369963369960.001115802366868050.00765457720660357
SP2#6668213.07676524692230.008330036536614940.0328022278051251
STAT1#6772315.52994062289940.000434088655175550.00404819939797118
STAT2#6773232.63188559322030.001379588775125520.0089810429523988
TCF7L2#693438.077632422353010.002978381685834620.0158574227613622



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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