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Coexpression cluster:C493: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;15:1.6953577709669:0.00416073088978701:0.0198267360221958
|tf_chipseq_enrich=POLR2A#5430;15:1.6953577709669:0.00416073088978701:0.0198267360221958
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|tfbs_overrepresentation_for_novel_motifs=0.38505,6.43496,0.373702,0.608931,0.643195,1.14145,0.267678,0.355351,1.87911,0.876098,0.189673,0.301621,0.106214,0.258863,1.06733,0.343795,0.450873,3.69078,0.11878,1.48579,0.11705,2.03425,0.592949,1.05327,0.44526,3.24285,1.01201,0.203923,0.651136,0.917888,0.174693,1.21322,3.34807,1.1517,0.943201,1.9715,0.0741766,1.14468,1.78132,1.29176,0.552378,0.163791,0.605973,2.14901,0.184169,0.135566,0.268517,0.182187,4.41488,0.0952386,1.58554,0.27764,0.450364,1.35889,0.691633,0.723091,0.322175,1.92306,0.369868,0.235655,0.519357,0.744306,0.631101,0.426924,0.284296,0.397545,0.774525,1.12911,0.473932,0.971498,0.916943,0.161173,0.441324,0.689771,0.101827,2.34544,1.74068,0.412445,0.471083,0.141103,0.0300846,0.426001,0.284019,0.157796,1.54937,0.0759684,0.0920104,3.65525,0.352635,1.2264,0.863265,0.617268,0.497892,0.775775,7.66712,0.0604965,2.11815,0.535841,0.356444,1.12155,2.35445,0.492893,0.530844,0.45406,0.387815,0.186536,0.440324,0.711872,0.14483,0.0851122,1.85196,0.528368,0.737452,0.196252,0.817503,0.0734112,0.190347,0.994069,0.395564,0.205172,0.682065,0.350633,0.209033,0.795647,0.923346,1.06222,0.726998,0.502315,0.721838,0.0609207,0.617901,2.27108,0.73532,0.290252,0.875585,0.335759,0.170663,1.74985,0.83506,1.67608,1.2779,0.799588,0.730043,1.31902,0.389296,0.23014,0.375295,1.51807,0.486639,0.197398,0.623601,0.116342,2.54664,0.142739,0.269969,1.0011,0.339339,0.0861459,0.445353,0.797033,0.798435,0.601304,0.470393,0.404939,0.402913,0.774125,0.182347,0.266654,3.41062
}}
}}

Revision as of 14:15, 26 November 2012


Full id: C493_Adipocyte_basal_Mesenchymal_Smooth_mesenchymal_Aortic_Multipotent



Phase1 CAGE Peaks

Hg19::chr11:117070079..117070097,+p1@TAGLN
Hg19::chr11:117070904..117070918,+p4@TAGLN
Hg19::chr11:117073740..117073758,+p3@TAGLN
Hg19::chr11:117073759..117073770,+p6@TAGLN
Hg19::chr11:117073868..117073881,+p2@TAGLN
Hg19::chr11:117074035..117074046,+p@chr11:117074035..117074046
+
Hg19::chr11:117074061..117074089,+p@chr11:117074061..117074089
+
Hg19::chr11:117074100..117074165,+p@chr11:117074100..117074165
+
Hg19::chr11:117074945..117074955,+p@chr11:117074945..117074955
+
Hg19::chr11:117074952..117074998,-p@chr11:117074952..117074998
-
Hg19::chr11:117074969..117074997,+p@chr11:117074969..117074997
+
Hg19::chr11:117075014..117075028,+p@chr11:117075014..117075028
+
Hg19::chr11:117075034..117075109,+p@chr11:117075034..117075109
+
Hg19::chr11:117075077..117075102,-p@chr11:117075077..117075102
-
Hg19::chr11:117075111..117075122,+p@chr11:117075111..117075122
+
Hg19::chr11:117075129..117075140,+p@chr11:117075129..117075140
+
Hg19::chr11:117075245..117075293,-p@chr11:117075245..117075293
-
Hg19::chr9:35685106..35685122,-p@chr9:35685106..35685122
-
Hg19::chr9:35685133..35685147,-p@chr9:35685133..35685147
-


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>

Uber Anatomy
Ontology termp-valuen
muscle tissue7.74e-2064
musculature7.74e-2064
musculature of body7.74e-2064
skeletal muscle tissue8.60e-1962
striated muscle tissue8.60e-1962
myotome8.60e-1962
dense mesenchyme tissue1.38e-1773
paraxial mesoderm5.44e-1772
presumptive paraxial mesoderm5.44e-1772
somite6.16e-1771
presomitic mesoderm6.16e-1771
presumptive segmental plate6.16e-1771
dermomyotome6.16e-1771
trunk paraxial mesoderm6.16e-1771
epithelial vesicle9.36e-1778
multilaminar epithelium8.13e-1683
mesenchyme1.10e-15160
entire embryonic mesenchyme1.10e-15160
trunk mesenchyme6.49e-15122
artery4.38e-1342
arterial blood vessel4.38e-1342
arterial system4.38e-1342
splanchnic layer of lateral plate mesoderm2.47e-1283
systemic artery8.02e-1233
systemic arterial system8.02e-1233
trunk7.39e-11199
epithelial tube open at both ends1.32e-0959
blood vessel1.32e-0959
blood vasculature1.32e-0959
vascular cord1.32e-0959
vasculature1.50e-0978
vascular system1.50e-0978
epithelial tube4.91e-09117
mesoderm9.26e-09315
mesoderm-derived structure9.26e-09315
presumptive mesoderm9.26e-09315
organism subdivision1.21e-08264
smooth muscle tissue1.31e-0815
circulatory system1.66e-08112
cardiovascular system3.96e-08109
vessel8.70e-0868
unilaminar epithelium3.68e-07148
primary circulatory organ5.29e-0727
multi-tissue structure6.17e-07342
multi-cellular organism6.90e-07656
blood vessel smooth muscle7.18e-0710
arterial system smooth muscle7.18e-0710
artery smooth muscle tissue7.18e-0710
aorta smooth muscle tissue7.18e-0710
Disease
Ontology termp-valuen
ovarian cancer2.22e-0714


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
POLR2A#5430151.69535777096690.004160730889787010.0198267360221958



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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