Coexpression cluster:C463: Difference between revisions

Revision as of 14:14, 26 November 2012

Full id: C463_Mesothelial_mesothelioma_Sertoli_mesenchymal_vagina_Cardiac_Fibroblast

Phase1 CAGE Peaks

Hg19::chr10:6622278..6622290,-	p6@PRKCQ
Hg19::chr11:116728907..116728948,+	p2@CU690121
Hg19::chr13:38091764..38091775,+	p@chr13:38091764..38091775 +
Hg19::chr13:38145825..38145840,-	p14@POSTN
Hg19::chr13:38148733..38148753,-	p@chr13:38148733..38148753 -
Hg19::chr13:97328912..97328917,+	p@chr13:97328912..97328917 +
Hg19::chr1:22469560..22469567,-	p3@WNT4
Hg19::chr20:6033732..6033760,-	p8@AB527789
Hg19::chr20:6034216..6034224,-	p@chr20:6034216..6034224 -
Hg19::chr20:6034506..6034518,-	p4@LRRN4
Hg19::chr20:61687988..61688007,-	p@chr20:61687988..61688007 -
Hg19::chr20:8101412..8101426,+	p@chr20:8101412..8101426 +
Hg19::chr20:8101451..8101452,+	p@chr20:8101451..8101452 +
Hg19::chr2:10454550..10454555,+	p@chr2:10454550..10454555 +
Hg19::chr2:220309299..220309306,+	p32@SPEG
Hg19::chr3:158450428..158450431,-	p9@RARRES1
Hg19::chr3:158450447..158450473,-	p4@RARRES1
Hg19::chr3:158450475..158450494,-	p6@RARRES1
Hg19::chr3:180707620..180707631,-	p3@DNAJC19
Hg19::chr4:146267392..146267393,-	p@chr4:146267392..146267393 -
Hg19::chr8:140663726..140663732,-	p@chr8:140663726..140663732 -

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:0032502	developmental process	0.00688389882661927
GO:0048856	anatomical structure development	0.0111239349841107
GO:0007275	multicellular organismal development	0.0126389772157664
GO:0008285	negative regulation of cell proliferation	0.0189097449991574
GO:0048513	organ development	0.0189097449991574
GO:0048731	system development	0.0285564188245063
GO:0032501	multicellular organismal process	0.0285564188245063
GO:0048806	genitalia development	0.0285564188245063
GO:0005578	proteinaceous extracellular matrix	0.0285564188245063
GO:0043681	protein import into mitochondrion	0.0285564188245063
GO:0004697	protein kinase C activity	0.0285564188245063
GO:0001565	phorbol ester receptor activity	0.0285564188245063
GO:0042127	regulation of cell proliferation	0.0285564188245063

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 disease_data

Cell Type
Ontology term	p-value	n
mesothelial cell	1.94e-16	19

Uber Anatomy
Ontology term	p-value	n
right ovary	7.49e-08	5

Disease
Ontology term	p-value	n
ovarian cancer	7.70e-22	14
female reproductive organ cancer	9.99e-12	27
reproductive organ cancer	5.69e-11	29

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

No analysis results for this cluster

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 8: / Line 8: @@
 |ontology_enrichment_uberon=UBERON:0002118!7.49e-08!5
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+|tfbs_overrepresentation_for_novel_motifs=0.102469,0.18095,0.324717,0.54841,0.563528,0.545716,1.25081,0.295736,0.536019,0.337519,0.496783,0.748251,1.35703,0.231159,0.264653,0.0881735,0.416635,0.434454,0.0930871,0.153235,0.324802,0.835453,0.533052,0.259643,0.124129,0.289541,0.173284,0.179098,0.965823,0.147924,0.462061,1.13801,0.362042,0.21322,0.831295,0.0501616,0.0600845,0.547612,0.738471,1.53913,0.21951,0.141543,0.0917928,0.262615,0.314233,0.744956,0.240368,0.158699,0.159934,0.078811,0.300624,0.249086,0.20228,0.515129,0.653159,0.233295,0.581687,0.603257,0.299101,0.209089,0.483605,0.679156,0.122235,0.393294,0.71007,0.364726,0.73513,1.08739,0.43915,0.930562,0.416257,0.130122,0.197136,0.651319,0.201153,0.353555,0.316622,0.379205,0.436366,0.120546,0.240865,1.01704,0.25519,1.70833,0.604277,1.50696,0.02106,0.140525,0.321213,1.18432,0.823081,0.579812,0.462581,0.0432003,0.0776122,1.55902,0.710498,0.499768,0.324895,0.24534,0.743127,0.45769,0.494867,0.419744,0.935363,0.48954,0.406348,0.228655,0.391767,0.897424,0.104554,0.492438,0.0955593,0.171884,0.777703,0.215264,1.16925,0.15094,0.362802,0.383976,0.64371,0.319278,0.541208,0.263675,0.882719,0.379837,1.91516,0.466912,0.683004,0.182525,0.580435,0.466574,0.696335,0.723221,0.835304,0.268768,0.147939,0.179476,0.795107,1.6331,1.23566,0.759951,0.236178,0.496668,0.356718,0.589128,0.343142,1.4753,0.139503,0.370558,0.507246,0.446854,0.58078,0.81624,0.678325,0.959994,0.308372,0.247915,0.124164,0.107739,0.758809,0.564094,1.11126,0.109525,0.36994,0.708093,0.344454,1.24712,1.44474
 }}

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Coexpression cluster:C463: Difference between revisions

From FANTOM5_SSTAR

Revision as of 14:14, 26 November 2012

Phase1 CAGE Peaks

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