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Coexpression cluster:C428: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;10:3.912154482128:8.29586753557824e-05:0.00124645678254676!GATA2#2624;16:8.86603946682017:2.93735337981159e-13:4.38248928048775e-11!JUN#3725;11:5.98439657024781:4.60970771361611e-07:2.18337081134854e-05!POLR2A#5430;21:1.96071811772693:8.35962402405614e-06:0.000230971104086878
|tf_chipseq_enrich=FOS#2353;10:3.912154482128:8.29586753557824e-05:0.00124645678254676!GATA2#2624;16:8.86603946682017:2.93735337981159e-13:4.38248928048775e-11!JUN#3725;11:5.98439657024781:4.60970771361611e-07:2.18337081134854e-05!POLR2A#5430;21:1.96071811772693:8.35962402405614e-06:0.000230971104086878
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|tfbs_overrepresentation_for_novel_motifs=0.292983,0.123941,0.0831821,0.495534,0.495107,0.492946,0.21518,0.464803,0.241904,0.256649,0.145297,1.2761,0.849493,0.207164,0.2271,0.546223,0.386278,0.164243,0.917208,0.371406,1.48582,0.200039,0.159229,0.061867,0.704829,0.263074,0.0499389,0.157865,0.0653771,0.115495,0.132203,0.416977,0.30708,0.5726,0.0500279,0.0305241,0.0488212,0.16489,0.0404254,0.082891,0.185583,0.122756,0.239836,0.84226,0.335547,0.0986693,0.215945,0.138738,0.055405,0.232836,0.273745,0.637443,0.290248,1.21241,0.61862,0.209199,0.512266,0.548346,0.422864,0.18619,0.451758,0.217609,0.0982927,0.363534,0.230363,0.892008,0.699678,1.04962,0.408258,0.893579,0.369304,0.257112,0.0675022,0.616804,0.0606565,0.290509,0.257418,0.349828,0.405538,0.689568,0.197082,0.362659,0.230109,1.11528,0.570388,0.00360896,0.113157,0.230646,0.293613,1.14619,0.786844,0.546282,0.43117,0.321513,0.0643605,0.348406,0.186686,0.467605,0.297172,0.554934,0.36371,0.426385,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.620092,0.460417,0.275626,0.89987,0.741849,0.181704,0.0459163,0.131498,0.333893,0.933551,0.60929,0.79308,0.162396,0.238235,0.846043,0.350442,0.605496,0.435409,0.648109,0.350382,0.546896,0.133891,0.66129,1.23665,0.798972,0.0344724,0.403911,0.478286,0.759101,1.59408,1.19737,0.724259,0.211948,2.04307,0.327989,0.181235,0.314828,1.43649,0.7692,0.1339,0.869011,0.0057425,0.547236,0.0910114,0.620941,0.922839,0.769146,0.211649,0.106679,0.30612,0.723128,0.530809,0.404879,0.310552,0.340824,0.649817,0.121873,0.214247,0.0515206
}}
}}

Revision as of 14:12, 26 November 2012


Full id: C428_Endothelial_Renal_Lymphatic_Hepatic_adipose_heart_breast



Phase1 CAGE Peaks

Hg19::chr10:13908291..13908320,-p@chr10:13908291..13908320
-
Hg19::chr12:6233727..6233738,-p5@VWF
Hg19::chr12:6233757..6233771,-p4@VWF
Hg19::chr12:6233828..6233843,-p1@VWF
Hg19::chr12:6234045..6234103,-p6@VWF
Hg19::chr12:71031185..71031215,-p1@PTPRB
Hg19::chr12:71031220..71031229,-p10@PTPRB
Hg19::chr12:71031247..71031262,-p7@PTPRB
Hg19::chr12:80084018..80084035,-p17@PAWR
Hg19::chr16:75285224..75285236,-p@chr16:75285224..75285236
-
Hg19::chr1:208063620..208063634,-p4@CD34
Hg19::chr21:39870339..39870443,-p1@ERG
Hg19::chr21:39875765..39875785,+p@chr21:39875765..39875785
+
Hg19::chr2:225266743..225266773,-p1@FAM124B
Hg19::chr2:225266813..225266830,-p2@FAM124B
Hg19::chr2:33661382..33661445,+p3@RASGRP3
Hg19::chr4:56814149..56814167,-p@chr4:56814149..56814167
-
Hg19::chr4:56814168..56814203,-p@chr4:56814168..56814203
-
Hg19::chr5:61874637..61874685,+p1@LRRC70
p2@IPO11
Hg19::chr5:66124590..66124644,+p2@MAST4
Hg19::chr7:11871574..11871633,-p3@THSD7A
Hg19::chr9:139538920..139538940,-p@chr9:139538920..139538940
-
Hg19::chrX:10544942..10544977,-p5@MID1


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

GO IDGO nameFDR corrected p-value
GO:0019899enzyme binding0.0128383398671892
GO:0005515protein binding0.0185725221551354
GO:0033093Weibel-Palade body0.0196043800777111
GO:0031091platelet alpha granule0.0294031075667311
GO:0046582Rap GTPase activator activity0.0352795745910804
GO:0002020protease binding0.0391949118586822
GO:0001948glycoprotein binding0.0499485389194682
GO:0043687post-translational protein modification0.0499485389194682



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
adult organism4.03e-56114
anatomical conduit1.27e-30240
tube3.49e-28192
blood vessel endothelium5.85e-2618
endothelium5.85e-2618
cardiovascular system endothelium5.85e-2618
anatomical cluster1.04e-24373
neural tube1.56e-2456
neural rod1.56e-2456
future spinal cord1.56e-2456
neural keel1.56e-2456
regional part of nervous system4.24e-2253
regional part of brain4.24e-2253
simple squamous epithelium5.44e-2022
regional part of forebrain2.54e-1841
forebrain2.54e-1841
anterior neural tube2.54e-1841
future forebrain2.54e-1841
neural plate3.03e-1882
presumptive neural plate3.03e-1882
structure with developmental contribution from neural crest2.36e-17132
squamous epithelium8.54e-1725
neurectoderm8.93e-1786
epithelium7.37e-16306
cell layer1.92e-15309
brain2.79e-1568
future brain2.79e-1568
vessel6.10e-1568
brain grey matter8.92e-1534
gray matter8.92e-1534
central nervous system9.10e-1581
telencephalon2.04e-1434
splanchnic layer of lateral plate mesoderm5.37e-1483
endothelial tube1.21e-139
arterial system endothelium1.21e-139
endothelium of artery1.21e-139
ecto-epithelium2.76e-13104
regional part of telencephalon3.46e-1332
cerebral hemisphere5.38e-1332
circulatory system2.62e-12112
nervous system3.83e-1289
vasculature1.20e-1178
vascular system1.20e-1178
regional part of cerebral cortex2.79e-1122
neocortex3.91e-1120
epithelial tube open at both ends7.18e-1159
blood vessel7.18e-1159
blood vasculature7.18e-1159
vascular cord7.18e-1159
multi-cellular organism7.67e-11656
cardiovascular system1.40e-10109
pre-chordal neural plate1.42e-1061
anatomical system1.74e-10624
anatomical group2.08e-10625
epithelial tube6.92e-10117
multi-tissue structure8.16e-10342
compound organ9.85e-1068
organ system subdivision1.37e-09223
cerebral cortex1.94e-0925
pallium1.94e-0925
lymphoid system9.54e-0910
embryonic structure4.84e-08564
organ part6.42e-08218
germ layer7.31e-08560
germ layer / neural crest7.31e-08560
embryonic tissue7.31e-08560
presumptive structure7.31e-08560
germ layer / neural crest derived structure7.31e-08560
epiblast (generic)7.31e-08560
vein7.67e-089
venous blood vessel7.67e-089
venous system7.67e-089
embryo8.58e-08592
developing anatomical structure1.16e-07581
posterior neural tube2.06e-0715
chordal neural plate2.06e-0715
primary circulatory organ2.62e-0727
lymphatic vessel3.21e-078
lymph vasculature3.21e-078
lymphatic part of lymphoid system3.21e-078
neural nucleus3.23e-079
nucleus of brain3.23e-079
brainstem5.96e-076


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
FOS#2353103.9121544821288.29586753557824e-050.00124645678254676
GATA2#2624168.866039466820172.93735337981159e-134.38248928048775e-11
JUN#3725115.984396570247814.60970771361611e-072.18337081134854e-05
POLR2A#5430211.960718117726938.35962402405614e-060.000230971104086878



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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