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Coexpression cluster:C2895: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513673978931347!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999375616041047!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240641108186192!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016127018762483!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192130076410794!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390878211137204!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186631944458037!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283161605728065!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00308039916205958!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.0076941795672089!NR2C2#7182;4:32.6146109052409:8.82887529809196e-07:3.82446664146589e-05!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227766420159063!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798133950706665!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297816281782426!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140406125918807!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245059543947485!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115778850902665!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509144203078231!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342621512932702!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249971642345592
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513673978931347!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999375616041047!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240641108186192!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.016127018762483!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192130076410794!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390878211137204!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186631944458037!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0283161605728065!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00308039916205958!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.0076941795672089!NR2C2#7182;4:32.6146109052409:8.82887529809196e-07:3.82446664146589e-05!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227766420159063!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798133950706665!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297816281782426!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140406125918807!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245059543947485!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115778850902665!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509144203078231!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342621512932702!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249971642345592
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}}
}}

Revision as of 15:47, 26 November 2012


Full id: C2895_immature_Mallassezderived_mesenchymal_CD14_Fibroblast_migratory_Endothelial



Phase1 CAGE Peaks

Hg19::chr7:39663146..39663225,+p1@RALA
Hg19::chr7:39663255..39663276,+p3@RALA
Hg19::chr7:39663286..39663317,+p2@RALA
Hg19::chr7:39663534..39663558,+p5@RALA


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>disease_data<br>


Cell Type
Ontology termp-valuen
mesodermal cell1.82e-19121
somatic cell2.35e-16588
animal cell2.46e-15679
eukaryotic cell2.46e-15679
endothelial cell of vascular tree2.29e-1324
somatic stem cell2.84e-13433
multi fate stem cell3.79e-13427
endothelial cell6.75e-1336
stem cell1.21e-12441
muscle precursor cell6.07e-1158
myoblast6.07e-1158
multi-potent skeletal muscle stem cell6.07e-1158
native cell1.11e-10722
blood vessel endothelial cell1.71e-1018
embryonic blood vessel endothelial progenitor cell1.71e-1018
vascular associated smooth muscle cell1.98e-1032
lining cell2.65e-1058
barrier cell2.65e-1058
muscle cell3.01e-1055
fibroblast3.30e-1076
embryonic cell3.44e-10250
meso-epithelial cell7.45e-1045
defensive cell3.08e-0948
phagocyte3.08e-0948
smooth muscle cell3.64e-0943
smooth muscle myoblast3.64e-0943
electrically responsive cell5.86e-0961
electrically active cell5.86e-0961
classical monocyte1.66e-0842
CD14-positive, CD16-negative classical monocyte1.66e-0842
contractile cell8.44e-0859
stuff accumulating cell2.96e-0787
macrophage dendritic cell progenitor4.06e-0761
cardiocyte4.88e-0716
Uber Anatomy
Ontology termp-valuen
vessel2.86e-2068
epithelial tube open at both ends1.02e-1859
blood vessel1.02e-1859
blood vasculature1.02e-1859
vascular cord1.02e-1859
vasculature1.84e-1878
vascular system1.84e-1878
splanchnic layer of lateral plate mesoderm1.94e-1783
artery1.39e-1642
arterial blood vessel1.39e-1642
arterial system1.39e-1642
mesoderm3.00e-13315
mesoderm-derived structure3.00e-13315
presumptive mesoderm3.00e-13315
systemic artery5.77e-1333
systemic arterial system5.77e-1333
cardiovascular system3.03e-12109
musculoskeletal system1.08e-11167
circulatory system7.19e-11112
blood vessel endothelium1.71e-1018
endothelium1.71e-1018
cardiovascular system endothelium1.71e-1018
aorta1.32e-0921
aortic system1.32e-0921
epithelial tube1.62e-09117
somite2.40e-0971
presomitic mesoderm2.40e-0971
presumptive segmental plate2.40e-0971
dermomyotome2.40e-0971
trunk paraxial mesoderm2.40e-0971
skeletal muscle tissue5.11e-0962
striated muscle tissue5.11e-0962
myotome5.11e-0962
multilaminar epithelium5.18e-0983
simple squamous epithelium5.67e-0922
paraxial mesoderm5.68e-0972
presumptive paraxial mesoderm5.68e-0972
dense mesenchyme tissue5.98e-0973
lateral plate mesoderm6.38e-09203
muscle tissue1.06e-0864
musculature1.06e-0864
musculature of body1.06e-0864
epithelial vesicle1.48e-0878
squamous epithelium6.47e-0825
unilaminar epithelium1.10e-07148
Disease
Ontology termp-valuen
ovarian cancer9.52e-0814


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#90546.336201576962630.0006203100587215640.00513673978931347
E2F6#187645.017155731697390.00157802193473060.00999375616041047
EBF1#187936.679850134926750.005184294118278910.0240641108186192
ELF1#199744.258097958807540.003041525565781240.016127018762483
ETS1#211337.296570691651750.00400857377511390.0192130076410794
GABPB1#255347.067683836182170.0004006876864423170.00390878211137204
HEY1#2346244.040111043105710.00375304636917980.0186631944458037
HMGN3#932436.133910792512940.006640696683324720.0283161605728065
IRF1#365947.63716375356390.0002938853996185490.00308039916205958
NFKB1#479045.488063424193840.001102199566301980.0076941795672089
NR2C2#7182432.61461090524098.82887529809196e-073.82446664146589e-05
POU2F2#545236.829593043306890.004860473775203740.0227766420159063
SIN3A#2594245.408884726815140.001168172384885160.00798133950706665
SIX5#147912417.0867153554591.17257016123224e-050.000297816281782426
TAF7#687938.574802053692940.00250055433515240.0140406125918807
TBP#690843.706770687096390.005296377814784350.0245059543947485
TCF7L2#6934410.77017656313737.42969445082454e-050.00115778850902665
USF1#739146.361499277207960.0006105011399140830.00509144203078231
ZBTB7A#5134135.513931980906920.009038352821081090.0342621512932702
ZNF263#1012748.221841637010680.0002187871180958320.00249971642345592



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.