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Difference between revisions of "Coexpression cluster:C3592"

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|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000221974090734091
 
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000221974090734091
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,1.40888,0.452865,0.824321,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,1.96502,0.645155,0.388328,0.795576,2.72118,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,2.42838,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,3.62494,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,2.82894,0.684398,0.830777,1.58942,0.594137,0.188952,1.86486,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,4.14226,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.265282
 
}}
 
}}

Revision as of 07:13, 26 November 2012


Full id: C3592_Fibroblast_schwannoma_basal_salivary_mesenchymal_large_Multipotent



Phase1 CAGE Peaks

Hg19::chr16:82660560..82660585,+p1@CDH13
Hg19::chr16:82660594..82660607,+p3@CDH13
Hg19::chr16:82660635..82660650,+p2@CDH13


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
epithelium3.39e-19306
cell layer5.10e-19309
anatomical cluster1.70e-18373
vasculature2.08e-1878
vascular system2.08e-1878
vessel1.89e-1768
anatomical conduit2.31e-17240
splanchnic layer of lateral plate mesoderm5.53e-1783
multi-cellular organism9.74e-17656
circulatory system2.68e-15112
multi-tissue structure4.64e-15342
epithelial tube open at both ends6.31e-1559
blood vessel6.31e-1559
blood vasculature6.31e-1559
vascular cord6.31e-1559
anatomical system1.28e-14624
anatomical group2.37e-14625
cardiovascular system2.92e-14109
multilaminar epithelium1.21e-1383
surface structure1.53e-1299
paraxial mesoderm1.91e-1272
presumptive paraxial mesoderm1.91e-1272
epithelial tube2.00e-12117
somite2.89e-1271
presomitic mesoderm2.89e-1271
presumptive segmental plate2.89e-1271
dermomyotome2.89e-1271
trunk paraxial mesoderm2.89e-1271
dense mesenchyme tissue2.91e-1273
epithelial vesicle3.70e-1278
artery1.27e-1142
arterial blood vessel1.27e-1142
arterial system1.27e-1142
skeletal muscle tissue1.53e-1162
striated muscle tissue1.53e-1162
myotome1.53e-1162
tube2.94e-11192
muscle tissue3.63e-1164
musculature3.63e-1164
musculature of body3.63e-1164
structure with developmental contribution from neural crest7.83e-10132
developing anatomical structure1.06e-09581
unilaminar epithelium1.60e-09148
organism subdivision3.01e-09264
systemic artery3.13e-0933
systemic arterial system3.13e-0933
embryonic structure3.38e-09564
primary circulatory organ4.63e-0927
embryo8.85e-09592
germ layer3.40e-08560
germ layer / neural crest3.40e-08560
embryonic tissue3.40e-08560
presumptive structure3.40e-08560
germ layer / neural crest derived structure3.40e-08560
epiblast (generic)3.40e-08560
heart6.60e-0824
primitive heart tube6.60e-0824
primary heart field6.60e-0824
anterior lateral plate mesoderm6.60e-0824
heart tube6.60e-0824
heart primordium6.60e-0824
cardiac mesoderm6.60e-0824
cardiogenic plate6.60e-0824
heart rudiment6.60e-0824
mesenchyme8.50e-08160
entire embryonic mesenchyme8.50e-08160
compound organ1.11e-0768
trunk mesenchyme1.15e-07122
ectoderm-derived structure2.90e-07171
ectoderm2.90e-07171
presumptive ectoderm2.90e-07171
skin of body3.49e-0741
integument3.73e-0746
integumental system3.73e-0746
aorta8.91e-0721
aortic system8.91e-0721
Disease
Ontology termp-valuen
ovarian cancer3.62e-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
SUZ12#23512350.11578091106297.93834897779404e-060.000221974090734091



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.