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Coexpression cluster:C1863: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353036190789305!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276620936477782!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.001365671537478!NRF1#4899;5:12.2102794477109:3.68220991173981e-06:0.000120742957919056!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117064056494025!RFX5#5993;4:9.63832866175608:0.00022148012581572:0.00249742635068754!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248253591970516!SP1#6667;5:5.6983813781409:0.00016639184371255:0.0020439658627964!SREBF1#6720;5:47.0058494404883:4.34669369311096e-09:3.54106351493616e-07!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919451319186933!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361210584499668!TFAP2A#7020;5:16.518634373045:8.12390055913032e-07:3.53964142884861e-05!TFAP2C#7022;5:10.8092286098602:6.77323239348459e-06:0.000197319279760987!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136907810277195!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.43282816046753e-05!ZBTB7A#51341;5:7.3519093078759:4.65425347594289e-05:0.000816127566779717!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111645651716066
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353036190789305!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276620936477782!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.001365671537478!NRF1#4899;5:12.2102794477109:3.68220991173981e-06:0.000120742957919056!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117064056494025!RFX5#5993;4:9.63832866175608:0.00022148012581572:0.00249742635068754!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248253591970516!SP1#6667;5:5.6983813781409:0.00016639184371255:0.0020439658627964!SREBF1#6720;5:47.0058494404883:4.34669369311096e-09:3.54106351493616e-07!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919451319186933!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361210584499668!TFAP2A#7020;5:16.518634373045:8.12390055913032e-07:3.53964142884861e-05!TFAP2C#7022;5:10.8092286098602:6.77323239348459e-06:0.000197319279760987!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136907810277195!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.43282816046753e-05!ZBTB7A#51341;5:7.3519093078759:4.65425347594289e-05:0.000816127566779717!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111645651716066
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}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1863_Multipotent_aorta_smooth_Olfactory_Chondrocyte_Preadipocyte_mesodermal



Phase1 CAGE Peaks

Hg19::chr20:17550489..17550543,+p3@DSTN
Hg19::chr20:17550544..17550559,+p6@DSTN
Hg19::chr20:17550575..17550596,+p5@DSTN
Hg19::chr20:17550691..17550782,+p1@DSTN
Hg19::chr20:17550786..17550804,+p2@DSTN


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
multi-tissue structure2.54e-20342
organism subdivision1.59e-19264
multi-cellular organism1.77e-16656
anatomical cluster1.54e-15373
trunk3.59e-14199
anatomical system4.80e-13624
anatomical group1.05e-12625
mesenchyme3.64e-12160
entire embryonic mesenchyme3.64e-12160
digestive system1.85e-11145
digestive tract1.85e-11145
primitive gut1.85e-11145
endoderm-derived structure2.59e-11160
endoderm2.59e-11160
presumptive endoderm2.59e-11160
organ7.86e-11503
trunk mesenchyme1.36e-09122
organ part1.42e-09218
cell layer2.62e-09309
epithelium3.85e-09306
embryo4.81e-09592
developing anatomical structure7.55e-09581
subdivision of trunk8.79e-09112
surface structure2.56e-0899
primordium5.86e-08160
embryonic structure8.23e-08564
subdivision of digestive tract8.71e-08118
muscle tissue2.78e-0764
musculature2.78e-0764
musculature of body2.78e-0764
anatomical conduit4.58e-07240
germ layer5.40e-07560
germ layer / neural crest5.40e-07560
embryonic tissue5.40e-07560
presumptive structure5.40e-07560
germ layer / neural crest derived structure5.40e-07560
epiblast (generic)5.40e-07560
respiratory system8.29e-0774
epithelial vesicle8.95e-0778
organ system subdivision9.07e-07223
skeletal muscle tissue9.19e-0762
striated muscle tissue9.19e-0762
myotome9.19e-0762


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
E2F1#186954.907389214879320.0003512818099256460.00353036190789305
MYC#460955.22228187160940.0002573944848850610.00276620936477782
NR3C1#2908411.97841866493849.4122920812787e-050.001365671537478
NRF1#4899512.21027944771093.68220991173981e-060.000120742957919056
PAX5#507956.669565531177837.57493746384605e-050.00117064056494025
RFX5#599349.638328661756080.000221480125815720.00249742635068754
SIN3A#2594255.408884726815140.0002159522671657270.00248253591970516
SP1#666755.69838137814090.000166391843712550.0020439658627964
SREBF1#6720547.00584944048834.34669369311096e-093.54106351493616e-07
TBP#690853.706770687096390.001428755106721120.00919451319186933
TCF12#693848.507571921749140.0003614215578492260.00361210584499668
TFAP2A#7020516.5186343730458.12390055913032e-073.53964142884861e-05
TFAP2C#7022510.80922860986026.77323239348459e-060.000197319279760987
USF1#739156.361499277207969.59569864925045e-050.00136907810277195
USF2#7392512.99219738506962.69963551658264e-069.43282816046753e-05
ZBTB7A#5134157.35190930787594.65425347594289e-050.000816127566779717
ZEB1#6935310.13305921052630.001895556924357070.0111645651716066



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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