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Difference between revisions of "Coexpression cluster:C2395"

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|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346401725392249!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297250491693814!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112841544281043!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386820506743765!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433792710309348!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499279122703509!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342360557914148
 
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346401725392249!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297250491693814!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112841544281043!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386820506743765!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433792710309348!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499279122703509!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342360557914148
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,2.60868,1.42279,0.505745,0.731221,0.528529,0.632849,0.892087,1.53358,1.72987,0.537869,0.806311,1.63433,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,1.99838,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,2.45549,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.859396,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,0.393155,1.63159,0.988625,0.444962,1.31973,0.932085,0.736652,4.72834,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.00378
 
}}
 
}}

Revision as of 06:28, 26 November 2012


Full id: C2395_Mesenchymal_Adipocyte_retina_Retinal_Melanocyte_Hepatocyte_mature



Phase1 CAGE Peaks

Hg19::chr17:1665279..1665295,+p2@SERPINF1
Hg19::chr17:1665306..1665317,+p3@SERPINF1
Hg19::chr17:1665345..1665362,+p1@SERPINF1
Hg19::chr17:1674352..1674377,+p@chr17:1674352..1674377
+


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>


Cell Type
Ontology termp-valuen
fat cell6.07e-1015
fibroblast2.67e-0976
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.14e-14656
adult organism5.93e-14114
anatomical group1.21e-11625
anatomical system2.89e-11624
tissue1.46e-10773
multi-tissue structure1.73e-10342
germ layer2.10e-10560
germ layer / neural crest2.10e-10560
embryonic tissue2.10e-10560
presumptive structure2.10e-10560
germ layer / neural crest derived structure2.10e-10560
epiblast (generic)2.10e-10560
embryonic structure5.89e-10564
organism subdivision7.75e-09264
developing anatomical structure1.03e-08581
embryo1.44e-08592
trunk mesenchyme3.01e-08122
dense mesenchyme tissue3.06e-0873
paraxial mesoderm7.29e-0872
presumptive paraxial mesoderm7.29e-0872
mesenchyme7.66e-08160
entire embryonic mesenchyme7.66e-08160
organ8.58e-08503
somite9.53e-0871
presomitic mesoderm9.53e-0871
presumptive segmental plate9.53e-0871
dermomyotome9.53e-0871
trunk paraxial mesoderm9.53e-0871
muscle tissue1.58e-0764
musculature1.58e-0764
musculature of body1.58e-0764
structure with developmental contribution from neural crest2.06e-07132
skeletal muscle tissue3.69e-0762
striated muscle tissue3.69e-0762
myotome3.69e-0762


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
ATF3#467316.84738089450660.0003409986823655640.00346401725392249
CEBPB#105135.978360719368610.007153832484726970.0297250491693814
JUN#372539.384621894252250.001918994502030470.0112841544281043
JUND#372735.245997956403270.01043432751748420.0386820506743765
RXRA#6256315.055962854350.0004758307997303580.00433792710309348
TRIM28#10155313.94289378394690.0005972858184258420.00499279122703509
ZBTB7A#5134135.513931980906920.009038352821081090.0342360557914148



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.