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Difference between revisions of "Coexpression cluster:C1542"

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|tf_chipseq_enrich=FOS#2353;6:8.9979553088944:1.88302066097805e-06:6.94914469299952e-05!GATA2#2624;6:12.744931733554:2.33109997620343e-07:1.22772440955476e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380772186362513
 
|tf_chipseq_enrich=FOS#2353;6:8.9979553088944:1.88302066097805e-06:6.94914469299952e-05!GATA2#2624;6:12.744931733554:2.33109997620343e-07:1.22772440955476e-05!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380772186362513
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.44418,7.89797,0.436508,0.58616,0.393082,0.584466,1.59238,2.09599,0.267027,0.555913,0.553339,0.707204,1.85338,0.650887,1.01544,0.415981,0.889639,0.336106,0.664996,0.800617,0.436569,2.73331,0.576478,0.387783,0.483957,0.730467,1.10781,0.574247,0.396295,1.04549,0.530785,0.92701,1.48187,0.225641,0.35719,0.577216,0.35388,0.585658,1.5795,0.248856,0.355745,0.513952,0.323162,0.390088,0.636689,0.468392,0.66382,0.542147,0.304272,1.81235,0.745008,0.675919,2.05902,1.00488,1.15929,0.653901,0.400834,0.62023,4.83244,0.619193,0.968558,0.666252,1.35522,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,1.17153,1.75965,2.39115,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.181326,1.29353,1.02636,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,1.53398,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,1.65925,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,5.29188,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,0.0926553,1.07915,1.32317,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.48859
 
}}
 
}}

Revision as of 05:57, 26 November 2012


Full id: C1542_Fibroblast_ductal_liposarcoma_large_normal_mesenchymal_Myoblast



Phase1 CAGE Peaks

  Short description
Hg19::chr8:18942243..18942259,- p8@PSD3
Hg19::chr8:18942279..18942294,- p11@PSD3
Hg19::chr8:18942296..18942344,- p6@PSD3
Hg19::chr8:18942386..18942401,- p22@PSD3
Hg19::chr8:18942407..18942448,- p14@PSD3
Hg19::chr8:18942514..18942527,- p24@PSD3


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
fibroblast4.06e-2576
skin fibroblast9.82e-1623
multi fate stem cell2.47e-14427
somatic stem cell2.25e-13433
stem cell3.69e-12441
muscle precursor cell4.35e-1158
myoblast4.35e-1158
multi-potent skeletal muscle stem cell4.35e-1158
non-terminally differentiated cell1.01e-10106
muscle cell2.52e-0955
connective tissue cell8.29e-09361
contractile cell2.15e-0859
somatic cell7.29e-08588
mesenchymal cell1.26e-07354
motile cell1.96e-07386
stromal cell2.29e-0728
electrically responsive cell2.92e-0761
electrically active cell2.92e-0761
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue2.21e-1473
somite2.46e-1471
presomitic mesoderm2.46e-1471
presumptive segmental plate2.46e-1471
dermomyotome2.46e-1471
trunk paraxial mesoderm2.46e-1471
paraxial mesoderm6.95e-1472
presumptive paraxial mesoderm6.95e-1472
mesenchyme1.30e-13160
entire embryonic mesenchyme1.30e-13160
epithelial vesicle5.10e-1278
multilaminar epithelium2.34e-1183
muscle tissue2.21e-1064
musculature2.21e-1064
musculature of body2.21e-1064
integument3.25e-1046
integumental system3.25e-1046
connective tissue3.64e-10371
skeletal muscle tissue5.18e-1062
striated muscle tissue5.18e-1062
myotome5.18e-1062
skin of body5.39e-1041
trunk mesenchyme1.14e-09122
tissue1.88e-09773
surface structure3.05e-0999
multi-tissue structure4.94e-08342
dermis5.56e-079
dermatome5.56e-079
future dermis5.56e-079
musculoskeletal system8.89e-07167


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235368.99795530889441.88302066097805e-066.94914469299952e-05
GATA2#2624612.7449317335542.33109997620343e-071.22772440955476e-05
POLR2A#543062.147453176558070.01019570676818780.0380772186362513



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.