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Coexpression cluster:C2818: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513307679445539!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441051234817469!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106743639424062!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099870944637819!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010727782952899!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719176187376973!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000627875244496464!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186507617886739!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248510580275454!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142684777529632!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088938508129285!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000235096404628492!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000311885511279136!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157385561207106!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000828072517755306!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797768624239984!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249790876272159!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323106865693667!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000971589134255356!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244896800194033!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120224926685695!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115692538951791!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508819156902777!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682448329420941!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107011582774962!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.0024969847914775
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513307679445539!CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441051234817469!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106743639424062!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099870944637819!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.0010727782952899!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719176187376973!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000627875244496464!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186507617886739!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248510580275454!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142684777529632!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088938508129285!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000235096404628492!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000311885511279136!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157385561207106!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000828072517755306!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797768624239984!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249790876272159!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323106865693667!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000971589134255356!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244896800194033!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120224926685695!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115692538951791!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508819156902777!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000682448329420941!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107011582774962!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.0024969847914775
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}}
}}

Revision as of 15:44, 26 November 2012


Full id: C2818_Smooth_Multipotent_hepatic_Preadipocyte_mesothelioma_Fibroblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:172755199..172755219,-p3@STC2
Hg19::chr5:172755232..172755247,-p4@STC2
Hg19::chr5:172755410..172755426,-p1@STC2
Hg19::chr5:172755444..172755455,-p2@STC2


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
trunk2.00e-19199
organism subdivision6.71e-18264
artery7.69e-1542
arterial blood vessel7.69e-1542
arterial system7.69e-1542
unilaminar epithelium1.20e-13148
splanchnic layer of lateral plate mesoderm1.98e-1383
somite1.06e-1271
presomitic mesoderm1.06e-1271
presumptive segmental plate1.06e-1271
dermomyotome1.06e-1271
trunk paraxial mesoderm1.06e-1271
trunk mesenchyme1.68e-12122
multilaminar epithelium2.17e-1283
dense mesenchyme tissue3.33e-1273
epithelial vesicle3.70e-1278
paraxial mesoderm4.46e-1272
presumptive paraxial mesoderm4.46e-1272
skeletal muscle tissue5.37e-1262
striated muscle tissue5.37e-1262
myotome5.37e-1262
systemic artery5.79e-1233
systemic arterial system5.79e-1233
epithelial tube1.05e-11117
muscle tissue2.18e-1164
musculature2.18e-1164
musculature of body2.18e-1164
mesenchyme3.91e-11160
entire embryonic mesenchyme3.91e-11160
epithelial tube open at both ends1.10e-1059
blood vessel1.10e-1059
blood vasculature1.10e-1059
vascular cord1.10e-1059
vasculature1.46e-1078
vascular system1.46e-1078
surface structure1.17e-0999
vessel1.82e-0968
cell layer2.08e-08309
epithelium4.30e-08306
cardiovascular system7.38e-08109
circulatory system1.04e-07112
integument1.81e-0746
integumental system1.81e-0746
skin of body3.01e-0741
subdivision of trunk4.99e-07112
primordium6.87e-07160
multi-cellular organism6.92e-07656
thoracic segment of trunk8.95e-0752


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
CCNT2#90546.336201576962630.0006203100587215640.00513307679445539
CTCFL#140690314.80985576923080.0004996291767563340.00441051234817469
E2F1#186944.907389214879320.001724022357361790.0106743639424062
E2F6#187645.017155731697390.00157802193473060.0099870944637819
FOXA1#3169411.08141974938556.62943068949433e-050.0010727782952899
GTF2F1#2962412.73966087675773.79492332235515e-050.000719176187376973
HDAC2#3066413.41562023662633.0859005065161e-050.000627875244496464
HEY1#2346244.040111043105710.00375304636917980.0186507617886739
HMGN3#932448.178547723350590.0002234570284440470.00248510580275454
MXI1#460149.96157162875930.0001015224754950450.00142684777529632
MYC#460945.22228187160940.001344309395272740.0088938508129285
NFYA#4800418.42558069983058.67100748407158e-060.000235096404628492
NFYB#4801416.75979325353651.26678572070404e-050.000311885511279136
REST#597849.650028716128020.0001152825614219170.00157385561207106
RFX5#5993412.04791082719514.74457429336527e-050.000828072517755306
SIN3A#2594245.408884726815140.001168172384885160.00797768624239984
SPI1#668848.204323508522730.000220661881527680.00249790876272159
TAF1#687243.343046285745290.008005664898701650.0323106865693667
TAF7#6879411.43306940492395.85061525419808e-050.000971589134255356
TBP#690843.706770687096390.005296377814784350.0244896800194033
TCF12#6938410.63446490218647.8163066689251e-050.00120224926685695
TCF7L2#6934410.77017656313737.42969445082454e-050.00115692538951791
USF1#739146.361499277207960.0006105011399140830.00508819156902777
USF2#7392412.99219738506963.50833029870167e-050.000682448329420941
YY1#752844.911170749853860.00171871838055440.0107011582774962
ZNF263#1012748.221841637010680.0002187871180958320.0024969847914775



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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