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Coexpression cluster:C1608: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003688!1.79e-13!6;UBERON:0002358!1.79e-13!6;UBERON:0003684!1.79e-13!6;UBERON:0001178!1.79e-13!6;UBERON:0002190!3.99e-12!3;UBERON:0003978!5.58e-12!3;UBERON:0009751!5.58e-12!3;UBERON:0000946!5.58e-12!3;UBERON:0002523!5.58e-12!3;UBERON:0005983!5.58e-12!3;UBERON:0002165!5.58e-12!3;UBERON:0002062!5.58e-12!3;UBERON:0007280!5.58e-12!3;UBERON:0004457!1.59e-11!12;UBERON:0000042!1.59e-11!12;UBERON:0002135!1.25e-09!1;UBERON:0002146!1.36e-09!1;UBERON:0005623!1.36e-09!1;UBERON:0002072!1.27e-07!5
|ontology_enrichment_uberon=UBERON:0003688!1.79e-13!6;UBERON:0002358!1.79e-13!6;UBERON:0003684!1.79e-13!6;UBERON:0001178!1.79e-13!6;UBERON:0002190!3.99e-12!3;UBERON:0003978!5.58e-12!3;UBERON:0009751!5.58e-12!3;UBERON:0000946!5.58e-12!3;UBERON:0002523!5.58e-12!3;UBERON:0005983!5.58e-12!3;UBERON:0002165!5.58e-12!3;UBERON:0002062!5.58e-12!3;UBERON:0007280!5.58e-12!3;UBERON:0004457!1.59e-11!12;UBERON:0000042!1.59e-11!12;UBERON:0002135!1.25e-09!1;UBERON:0002146!1.36e-09!1;UBERON:0005623!1.36e-09!1;UBERON:0002072!1.27e-07!5
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,1.57627,1.15291,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,1.20439,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0938701
}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1608_Adipocyte_mature_heart_adipose_breast_skin_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr11:111717027..111717039,-p@chr11:111717027..111717039
-
Hg19::chr11:111794400..111794410,+p@chr11:111794400..111794410
+
Hg19::chr15:90224806..90224821,-p@chr15:90224806..90224821
-
Hg19::chr1:168698433..168698451,-p1@DPT
Hg19::chr2:218776086..218776090,-p@chr2:218776086..218776090
-


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 cell6.35e-6715
adipocyte of omentum tissue2.46e-263
adipocyte of breast3.16e-182
subcutaneous fat cell3.99e-123
stuff accumulating cell4.64e-1087
GAG secreting cell9.24e-099
carbohydrate secreting cell9.24e-099
Uber Anatomy
Ontology termp-valuen
omentum1.79e-136
peritoneum1.79e-136
abdominal cavity1.79e-136
visceral peritoneum1.79e-136
subcutaneous adipose tissue3.99e-123
valve5.58e-123
cardiac mesenchyme5.58e-123
cardial valve5.58e-123
tunica intima5.58e-123
heart layer5.58e-123
endocardium5.58e-123
endocardial cushion5.58e-123
presumptive endocardium5.58e-123
cavity lining1.59e-1112
serous membrane1.59e-1112
mitral valve1.25e-091
pulmonary valve1.36e-091
semi-lunar valve1.36e-091
hypodermis1.27e-075


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

No analysis results for this cluster

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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