Coexpression cluster:C1777: Difference between revisions

Revision as of 15:06, 26 November 2012

Full id: C1777_keratoacanthoma_esophagus_oral_Mammary_cervical_epidermoid_Corneal

Phase1 CAGE Peaks

Hg19::chr17:39673166..39673191,-	p@chr17:39673166..39673191 -
Hg19::chr17:39673387..39673422,-	p@chr17:39673387..39673422 -
Hg19::chr17:39674668..39674681,-	p8@KRT15
Hg19::chr17:39674800..39674821,-	p5@KRT15
Hg19::chr17:39675131..39675148,-	p1@KRT15

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 disease_data

Cell Type
Ontology term	p-value	n
endo-epithelial cell	2.15e-27	42
endodermal cell	1.67e-20	58
epithelial cell of alimentary canal	1.29e-18	20
respiratory epithelial cell	1.58e-11	13
duct epithelial cell	9.28e-11	3
branched duct epithelial cell	9.28e-11	3
tracheal epithelial cell	9.28e-11	3
tracheoblast	9.28e-11	3
epithelial cell	3.19e-10	253
stratified squamous epithelial cell	1.24e-09	6
keratin accumulating cell	1.24e-09	6
stratified epithelial cell	1.24e-09	6
keratinizing barrier epithelial cell	1.24e-09	6
epithelial fate stem cell	1.24e-09	6
stratified epithelial stem cell	1.24e-09	6
surface ectodermal cell	1.24e-09	6
squamous epithelial cell	8.16e-09	63
mammary gland epithelial cell	9.75e-09	4
corneal epithelial cell	2.28e-08	2
keratinocyte	6.98e-07	5

Uber Anatomy
Ontology term	p-value	n
neck	1.30e-20	10
orifice	5.10e-18	36
oral opening	6.81e-17	22
respiratory system	2.68e-16	74
mouth	1.06e-14	29
stomodeum	1.06e-14	29
mucosa of oral region	3.50e-14	4
respiratory system mucosa	3.50e-14	4
pharynx	6.04e-14	11
anterior region of body	1.24e-13	62
craniocervical region	1.24e-13	62
endoderm-derived structure	2.10e-13	160
endoderm	2.10e-13	160
presumptive endoderm	2.10e-13	160
surface structure	7.88e-13	99
mouth mucosa	3.28e-12	13
chordate pharynx	1.42e-11	10
pharyngeal region of foregut	1.42e-11	10
tongue	2.70e-11	3
gustatory system	2.70e-11	3
future tongue	2.70e-11	3
digestive system	3.73e-11	145
digestive tract	3.73e-11	145
primitive gut	3.73e-11	145
subdivision of head	9.17e-11	49
respiratory tract	3.24e-10	54
mucosa	8.38e-10	20
head	5.07e-09	56
mammary gland	9.75e-09	4
mammary bud	9.75e-09	4
mammary ridge	9.75e-09	4
mammary placode	9.75e-09	4
throat	3.03e-08	2
trachea	8.88e-08	7
respiratory airway	8.88e-08	7
segment of respiratory tract	1.16e-07	47
subdivision of digestive tract	2.37e-07	118
organism subdivision	8.86e-07	264

Disease
Ontology term	p-value	n
squamous cell carcinoma	3.93e-18	14

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 7: / Line 7: @@
 |ontology_enrichment_uberon=UBERON:0000974!1.30e-20!10;UBERON:0000161!5.10e-18!36;UBERON:0000166!6.81e-17!22;UBERON:0001004!2.68e-16!74;UBERON:0000165!1.06e-14!29;UBERON:0000930!1.06e-14!29;UBERON:0003343!3.50e-14!4;UBERON:0004785!3.50e-14!4;UBERON:0006562!6.04e-14!11;UBERON:0000153!1.24e-13!62;UBERON:0007811!1.24e-13!62;UBERON:0004119!2.10e-13!160;UBERON:0000925!2.10e-13!160;UBERON:0006595!2.10e-13!160;UBERON:0003102!7.88e-13!99;UBERON:0003729!3.28e-12!13;UBERON:0001042!1.42e-11!10;UBERON:0009145!1.42e-11!10;UBERON:0001723!2.70e-11!3;UBERON:0001033!2.70e-11!3;UBERON:0010056!2.70e-11!3;UBERON:0001007!3.73e-11!145;UBERON:0001555!3.73e-11!145;UBERON:0007026!3.73e-11!145;UBERON:0001444!9.17e-11!49;UBERON:0000065!3.24e-10!54;UBERON:0000344!8.38e-10!20;UBERON:0000033!5.07e-09!56;UBERON:0001911!9.75e-09!4;UBERON:0005333!9.75e-09!4;UBERON:0008425!9.75e-09!4;UBERON:0005311!9.75e-09!4;UBERON:0000341!3.03e-08!2;UBERON:0003126!8.88e-08!7;UBERON:0001005!8.88e-08!7;UBERON:0000072!1.16e-07!47;UBERON:0004921!2.37e-07!118;UBERON:0000475!8.86e-07!264
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+|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,1.70183,0.621241,0.778743,0.274093,0.721271,0.453496,1.20439,0.963929,0.395009,0.784337,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,1.38854,0.417272,1.62925,0.413782,0.654459,1.00769,0.301779,0.415749,0.580638,0.132849,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,3.52357,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,1.05945
 }}

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Coexpression cluster:C1777: Difference between revisions

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Revision as of 15:06, 26 November 2012

Phase1 CAGE Peaks

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0