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Coexpression cluster:C3722: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129583760015808!BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284445798133819!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321982894094702!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461994231260727!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761816830777024!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127993811877581!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186388376378257!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719990266211498!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029431239504124!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269466598756819!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276521440551184!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239585713596197!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246316266138924!SRF#6722;3:13.7971782621678:0.000380661502580019:0.0037491424620855!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613373634419482!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615695208597127!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190158125536137!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421433217268727!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329170426928691!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388851986373223
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129583760015808!BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284445798133819!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321982894094702!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461994231260727!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00761816830777024!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127993811877581!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186388376378257!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719990266211498!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029431239504124!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269466598756819!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276521440551184!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239585713596197!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246316266138924!SRF#6722;3:13.7971782621678:0.000380661502580019:0.0037491424620855!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613373634419482!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615695208597127!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190158125536137!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421433217268727!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329170426928691!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388851986373223
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}}
}}

Revision as of 16:18, 26 November 2012


Full id: C3722_Preadipocyte_mature_Adipocyte_Fibroblast_Hepatic_Smooth_Pericytes



Phase1 CAGE Peaks

Hg19::chr18:46065483..46065540,+p2@CTIF
Hg19::chr18:46065541..46065568,+p3@CTIF
Hg19::chr18:46065570..46065579,+p6@CTIF


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
cell layer4.11e-22309
epithelium4.59e-21306
anatomical cluster2.81e-20373
anatomical conduit2.58e-19240
multi-cellular organism6.59e-19656
tube4.80e-17192
multi-tissue structure8.14e-16342
splanchnic layer of lateral plate mesoderm2.01e-1583
anatomical system2.64e-15624
anatomical group5.71e-15625
vasculature7.73e-1578
vascular system7.73e-1578
epithelial tube7.32e-14117
trunk mesenchyme1.77e-12122
vessel5.15e-1268
structure with developmental contribution from neural crest5.25e-12132
epithelial vesicle6.63e-1278
epithelial tube open at both ends1.00e-1159
blood vessel1.00e-1159
blood vasculature1.00e-1159
vascular cord1.00e-1159
multilaminar epithelium1.97e-1183
organism subdivision2.10e-11264
dense mesenchyme tissue2.61e-1173
artery3.08e-1142
arterial blood vessel3.08e-1142
arterial system3.08e-1142
mesenchyme3.42e-11160
entire embryonic mesenchyme3.42e-11160
unilaminar epithelium4.69e-11148
paraxial mesoderm6.00e-1172
presumptive paraxial mesoderm6.00e-1172
somite1.22e-1071
presomitic mesoderm1.22e-1071
presumptive segmental plate1.22e-1071
dermomyotome1.22e-1071
trunk paraxial mesoderm1.22e-1071
ectoderm-derived structure1.27e-10171
ectoderm1.27e-10171
presumptive ectoderm1.27e-10171
skeletal muscle tissue1.36e-1062
striated muscle tissue1.36e-1062
myotome1.36e-1062
muscle tissue1.56e-1064
musculature1.56e-1064
musculature of body1.56e-1064
embryonic structure2.17e-10564
cardiovascular system2.38e-10109
germ layer3.57e-10560
germ layer / neural crest3.57e-10560
embryonic tissue3.57e-10560
presumptive structure3.57e-10560
germ layer / neural crest derived structure3.57e-10560
epiblast (generic)3.57e-10560
systemic artery6.06e-1033
systemic arterial system6.06e-1033
trunk6.92e-10199
circulatory system8.40e-10112
developing anatomical structure1.83e-09581
embryo9.74e-09592
organ part5.35e-08218
surface structure1.83e-0799
aorta2.82e-0721
aortic system2.82e-0721
ecto-epithelium9.83e-07104


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
ATF3#467322.46317452600878.81932387510763e-050.00129583760015808
BHLHE40#8553344.87181354697741.10603738662898e-050.000284445798133819
E2F6#187635.017155731697390.00791769806886330.0321982894094702
ELF1#199734.258097958807540.01295179875054610.0461994231260727
ETS1#211339.728760922202340.001085840092584840.00761816830777024
IRF1#365937.63716375356390.002244692747297240.0127993811877581
MAX#414936.452555509007120.003721913834265510.0186388376378257
MXI1#460139.96157162875930.001011470541259020.00719990266211498
MYC#460935.22228187160940.007020843755740150.029431239504124
NFKB1#479035.488063424193840.006049381815655430.0269466598756819
SIN3A#2594235.408884726815140.006318961977991520.0276521440551184
SIX5#147912317.0867153554590.0002004060546325010.00239585713596197
SP1#666735.69838137814090.005403962701712170.0246316266138924
SRF#6722313.79717826216780.0003806615025800190.0037491424620855
TCF7L2#6934310.77017656313730.0008003181298398380.00613373634419482
TFAP2C#7022310.80922860986020.0007916746575753130.00615695208597127
USF1#739136.361499277207960.00388404057290560.0190158125536137
USF2#7392312.99219738506960.0004558979393427810.00421433217268727
YY1#752834.911170749853860.008441455341808260.0329170426928691
ZNF143#7702313.50087655222790.0004062804962997170.00388851986373223



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.