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Coexpression cluster:C200: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C200_seminal_Cardiac_Smooth_Hair_submaxillary_Neutrophils_mixed
|full_id=C200_seminal_Cardiac_Smooth_Hair_submaxillary_Neutrophils_mixed
|id=C200
|id=C200

Revision as of 14:40, 12 September 2012


Full id: C200_seminal_Cardiac_Smooth_Hair_submaxillary_Neutrophils_mixed



Phase1 CAGE Peaks

Hg19::chr10:50911176..50911180,-p@chr10:50911176..50911180
-
Hg19::chr10:50911313..50911330,-p@chr10:50911313..50911330
-
Hg19::chr11:111691980..111692005,-p@chr11:111691980..111692005
-
Hg19::chr11:13285557..13285582,+p@chr11:13285557..13285582
+
Hg19::chr11:77597678..77597713,+p1@ENST00000516522
Hg19::chr11:85195010..85195053,+p2@ENST00000463796
Hg19::chr12:127650900..127650948,-p1@ENST00000488123
Hg19::chr12:127650961..127650963,-p4@ENST00000488123
Hg19::chr12:127650966..127650970,-p3@ENST00000488123
Hg19::chr12:127650982..127650997,-p2@ENST00000488123
Hg19::chr12:20704366..20704465,+p1@ENST00000459949
Hg19::chr12:34372645..34372687,-p1@ENST00000483424
Hg19::chr12:85562743..85562771,-p@chr12:85562743..85562771
-
Hg19::chr14:43722994..43723027,+p@chr14:43722994..43723027
+
Hg19::chr14:90341521..90341554,-p1@ENST00000471006
Hg19::chr16:33963051..33963078,+p@chr16:33963051..33963078
+
Hg19::chr16:33963085..33963113,+p@chr16:33963085..33963113
+
Hg19::chr16:33963114..33963125,+p@chr16:33963114..33963125
+
Hg19::chr16:33963205..33963248,+p@chr16:33963205..33963248
+
Hg19::chr16:33963307..33963381,+p@chr16:33963307..33963381
+
Hg19::chr16:33963702..33963740,+p@chr16:33963702..33963740
+
Hg19::chr16:33963885..33963944,+p@chr16:33963885..33963944
+
Hg19::chr19:24182441..24182447,-p@chr19:24182441..24182447
-
Hg19::chr19:24183089..24183138,-p@chr19:24183089..24183138
-
Hg19::chr19:24183260..24183291,-p@chr19:24183260..24183291
-
Hg19::chr19:24183404..24183444,-p@chr19:24183404..24183444
-
Hg19::chr19:24186160..24186198,-p@chr19:24186160..24186198
-
Hg19::chr19:42070281..42070329,-p@chr19:42070281..42070329
-
Hg19::chr19:42070456..42070481,-p@chr19:42070456..42070481
-
Hg19::chr19:43911276..43911313,+p@chr19:43911276..43911313
+
Hg19::chr19:43911674..43911688,+p@chr19:43911674..43911688
+
Hg19::chr1:237766403..237766436,+p@chr1:237766403..237766436
+
Hg19::chr1:237766565..237766606,+p@chr1:237766565..237766606
+
Hg19::chr1:237766669..237766688,+p@chr1:237766669..237766688
+
Hg19::chr1:91852815..91852953,-p1@ENST00000516420
Hg19::chr1:91852985..91853011,-p2@ENST00000516420
Hg19::chr1:91853019..91853049,-p@chr1:91853019..91853049
-
Hg19::chr21:15457277..15457318,-p@chr21:15457277..15457318
-
Hg19::chr21:15457426..15457442,-p@chr21:15457426..15457442
-
Hg19::chr2:133012497..133012510,-p@chr2:133012497..133012510
-
Hg19::chr2:133012853..133012916,-p@chr2:133012853..133012916
-
Hg19::chr2:133013392..133013403,-p@chr2:133013392..133013403
-
Hg19::chr2:133013454..133013486,-p@chr2:133013454..133013486
-
Hg19::chr2:133013686..133013716,-p@chr2:133013686..133013716
-
Hg19::chr2:133036537..133036585,-p@chr2:133036537..133036585
-
Hg19::chr2:133036692..133036736,-p@chr2:133036692..133036736
-
Hg19::chr2:133037053..133037081,-p@chr2:133037053..133037081
-
Hg19::chr2:133037423..133037469,-p@chr2:133037423..133037469
-
Hg19::chr2:133037552..133037583,-p@chr2:133037552..133037583
-
Hg19::chr2:133037595..133037612,-p@chr2:133037595..133037612
-
Hg19::chr2:159440737..159440770,-p@chr2:159440737..159440770
-
Hg19::chr2:191402684..191402709,-p@chr2:191402684..191402709
-
Hg19::chr2:191402749..191402790,-p1@ENST00000492032
Hg19::chr2:203211018..203211031,-p@chr2:203211018..203211031
-
Hg19::chr2:203211038..203211057,-p2@ENST00000473498
Hg19::chr2:78928720..78928755,+p@chr2:78928720..78928755
+
Hg19::chr2:78928877..78928888,+p@chr2:78928877..78928888
+
Hg19::chr2:78928923..78928950,+p@chr2:78928923..78928950
+
Hg19::chr4:107924792..107924829,-p@chr4:107924792..107924829
-
Hg19::chr4:76807171..76807211,+p1@ENST00000464639
Hg19::chr5:154788152..154788155,+p1@ENST00000485443
Hg19::chr6:144692233..144692263,-p@chr6:144692233..144692263
-
Hg19::chr7:104966296..104966333,+p1@ENST00000469253
Hg19::chr7:68527622..68527642,+p2@ENST00000517158
Hg19::chr7:80962970..80962986,+p@chr7:80962970..80962986
+
Hg19::chr7:80963063..80963113,+p@chr7:80963063..80963113
+
Hg19::chr8:21456056..21456083,+p@chr8:21456056..21456083
+
Hg19::chr8:46951861..46951876,-p@chr8:46951861..46951876
-
Hg19::chr8:46952011..46952037,-p@chr8:46952011..46952037
-
Hg19::chr8:56755211..56755245,-p@chr8:56755211..56755245
-
Hg19::chr8:56822005..56822038,-p1@ENST00000481252
Hg19::chr8:69218623..69218656,-p@chr8:69218623..69218656
-
Hg19::chr8:70602393..70602439,-p1@ENST00000516388
Hg19::chr8:70602464..70602479,-p2@ENST00000516388
Hg19::chr8:70602485..70602518,-p@chr8:70602485..70602518
-
Hg19::chr8:70602589..70602625,-p@chr8:70602589..70602625
-
Hg19::chr9:19278548..19278559,+p@chr9:19278548..19278559
+
Hg19::chr9:79186644..79186694,+p1@ENST00000463508
Hg19::chrX:108297392..108297444,+p@chrX:108297392..108297444
+
Hg19::chrX:108297652..108297666,+p@chrX:108297652..108297666
+
Hg19::chrX:108297700..108297742,+p@chrX:108297700..108297742
+
Hg19::chrX:108297778..108297814,+p@chrX:108297778..108297814
+
Hg19::chrX:47749756..47749774,-p1@ENST00000487797


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
lateral plate mesoderm5.07e-13216
mesoderm1.09e-10448
mesoderm-derived structure1.09e-10448
presumptive mesoderm1.09e-10448
adult organism1.34e-09115
circulatory system8.48e-09113
multi-cellular organism2.28e-08659
cardiovascular system4.34e-08110
musculoskeletal system7.55e-08167
vasculature7.91e-0879
vascular system7.91e-0879
vessel1.37e-0769
embryonic structure1.38e-07605
developing anatomical structure1.38e-07605
germ layer1.58e-07604
embryonic tissue1.58e-07604
presumptive structure1.58e-07604
epiblast (generic)1.58e-07604
anatomical system1.84e-07625
blood vessel2.41e-0760
epithelial tube open at both ends2.41e-0760
blood vasculature2.41e-0760
vascular cord2.41e-0760
anatomical group2.46e-07626
artery9.11e-0742
arterial blood vessel9.11e-0742
arterial system9.11e-0742
splanchnic layer of lateral plate mesoderm9.73e-0784


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

No analysis results for this cluster

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

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