Coexpression cluster:C1362: Difference between revisions

Revision as of 14:50, 26 November 2012

Full id: C1362_Preadipocyte_Adipocyte_Fibroblast_Mesenchymal_mesenchymal_Myoblast_Smooth

Phase1 CAGE Peaks

Hg19::chr12:54402694..54402705,+	p5@HOXC8
Hg19::chr12:54402729..54402743,+	p3@HOXC8
Hg19::chr12:54402745..54402788,+	p1@HOXC8
Hg19::chr12:54402790..54402805,+	p2@HOXC8
Hg19::chr12:54410639..54410659,+	p2@HOXC4 p2@HOXC5 p2@HOXC6
Hg19::chr12:54410664..54410684,+	p1@HOXC4 p1@HOXC5 p1@HOXC6

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

GO ID	GO name	FDR corrected p-value
GO:0043565	sequence-specific DNA binding	0.0289572869453141
GO:0003700	transcription factor activity	0.0355826006899583
GO:0007275	multicellular organismal development	0.0355826006899583
GO:0032502	developmental process	0.0355826006899583
GO:0006355	regulation of transcription, DNA-dependent	0.0355826006899583
GO:0006351	transcription, DNA-dependent	0.0355826006899583
GO:0032774	RNA biosynthetic process	0.0355826006899583
GO:0003677	DNA binding	0.0355826006899583
GO:0045449	regulation of transcription	0.0355826006899583
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0355826006899583
GO:0030182	neuron differentiation	0.0355826006899583
GO:0006350	transcription	0.0355826006899583
GO:0032501	multicellular organismal process	0.0355826006899583
GO:0010468	regulation of gene expression	0.0355826006899583
GO:0031323	regulation of cellular metabolic process	0.0355826006899583
GO:0048699	generation of neurons	0.0355826006899583
GO:0019222	regulation of metabolic process	0.0355826006899583
GO:0016070	RNA metabolic process	0.0355826006899583
GO:0022008	neurogenesis	0.0355826006899583

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 term	p-value	n
fat cell	6.85e-12	15
skin fibroblast	1.53e-11	23
preadipocyte	6.06e-11	12
fibroblast	9.20e-11	76
mesenchymal stem cell of adipose	1.99e-07	8
non-terminally differentiated cell	3.08e-07	106

Uber Anatomy
Ontology term	p-value	n
integument	3.96e-13	46
integumental system	3.96e-13	46
adipose tissue	3.39e-11	14
skin of body	2.48e-10	41
trunk	8.21e-09	199
mesenchyme	4.21e-08	160
entire embryonic mesenchyme	4.21e-08	160
body cavity or lining	3.58e-07	49
articulation	6.83e-07	8
skeletal joint	6.83e-07	8
articular system	6.83e-07	8

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	#promoters	Enrichment	p-value	q-value
CTCF#10664	4	3.57350424871668	0.0131663500723851	0.0466002587505026
SUZ12#23512	2	16.7052603036876	0.00566023468207957	0.0255587898292926

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.

@@ Line 9: / Line 9: @@
 |tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466002587505026!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255587898292926
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+|tfbs_overrepresentation_for_novel_motifs=0.44418,1.82196,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.94331,0.553339,0.707204,0.635275,1.56773,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,0.0880431,2.41159,0.387783,0.483957,1.73319,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,1.48187,0.225641,0.35719,0.316592,1.66498,0.585658,0.329602,0.248856,0.355745,0.513952,0.664116,1.01199,0.0393783,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,2.22199,1.59978,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,4.31331,1.15727,2.57543,0.206105,0.192925,0.84426,0.913168,3.09039,0.240887,0.86037,0.684313,0.272514,1.10535,0.181326,0.398737,0.181871,1.81827,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,2.10687,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,3.49606,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,2.18236,1.1919,0.866571,1.07876,0.53374,1.20639,1.65434,1.35529,33.0632,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,3.15765,0.136746,0.639143,1.07915,1.32317,0.665754,1.48627,0.755083,1.75096,3.11955,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.152397
 }}

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Coexpression cluster:C1362: Difference between revisions

From FANTOM5_SSTAR

Revision as of 14:50, 26 November 2012

Phase1 CAGE Peaks

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