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Coexpression cluster:C3626: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324873841426594
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324873841426594
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,2.1336,1.18351,0.820209,0.985163,1.11328,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,1.86765,1.21459,0.534793,0.439574,2.48753,0.137917,1.45286,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,6.48329,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,3.76231,23.4148,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,2.61709,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,4.47109,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,4.59952,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,5.47603,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
}}
}}

Revision as of 16:14, 26 November 2012


Full id: C3626_Pericytes_oral_Hair_Hepatic_Endothelial_Mesothelial_clear



Phase1 CAGE Peaks

Hg19::chr17:36609912..36609923,+p@chr17:36609912..36609923
+
Hg19::chr17:36609926..36609952,+p@chr17:36609926..36609952
+
Hg19::chr17:36609957..36609978,+p@chr17:36609957..36609978
+


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 layer2.05e-18309
vasculature9.85e-1878
vascular system9.85e-1878
epithelium1.54e-17306
epithelial tube8.19e-17117
organism subdivision2.31e-16264
anatomical cluster4.57e-16373
multi-tissue structure2.55e-15342
splanchnic layer of lateral plate mesoderm4.08e-1583
unilaminar epithelium1.14e-14148
vessel1.43e-1468
mesenchyme3.93e-13160
entire embryonic mesenchyme3.93e-13160
epithelial tube open at both ends5.28e-1359
blood vessel5.28e-1359
blood vasculature5.28e-1359
vascular cord5.28e-1359
epithelial vesicle3.19e-1278
multi-cellular organism3.66e-12656
anatomical system4.50e-12624
anatomical conduit5.38e-12240
anatomical group8.43e-12625
trunk1.02e-11199
multilaminar epithelium1.22e-1183
trunk mesenchyme1.37e-11122
circulatory system2.71e-11112
cardiovascular system5.10e-11109
organ part1.07e-10218
blood vessel endothelium1.11e-0918
endothelium1.11e-0918
cardiovascular system endothelium1.11e-0918
dense mesenchyme tissue1.91e-0973
somite1.94e-0971
presomitic mesoderm1.94e-0971
presumptive segmental plate1.94e-0971
dermomyotome1.94e-0971
trunk paraxial mesoderm1.94e-0971
surface structure2.97e-0999
paraxial mesoderm3.86e-0972
presumptive paraxial mesoderm3.86e-0972
simple squamous epithelium1.13e-0822
artery2.49e-0842
arterial blood vessel2.49e-0842
arterial system2.49e-0842
tube2.74e-08192
squamous epithelium4.01e-0825
skeletal muscle tissue1.03e-0762
striated muscle tissue1.03e-0762
myotome1.03e-0762
compound organ1.15e-0768
muscle tissue2.25e-0764
musculature2.25e-0764
musculature of body2.25e-0764
nephron epithelium4.59e-0715
renal tubule4.59e-0715
nephron tubule4.59e-0715
nephron4.59e-0715
uriniferous tubule4.59e-0715
nephrogenic mesenchyme4.59e-0715
organ component layer4.92e-0766
parenchyma6.52e-0715
endoderm-derived structure8.09e-07160
endoderm8.09e-07160
presumptive endoderm8.09e-07160
subdivision of head9.41e-0749


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#186934.907389214879320.008460985347239390.0324873841426594



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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