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Coexpression cluster:C1786: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001134!5.71e-22!62;UBERON:0002036!5.71e-22!62;UBERON:0003082!5.71e-22!62;UBERON:0002385!1.05e-20!64;UBERON:0001015!1.05e-20!64;UBERON:0000383!1.05e-20!64;UBERON:0007524!1.99e-19!73;UBERON:0002329!3.32e-19!71;UBERON:0003059!3.32e-19!71;UBERON:0007282!3.32e-19!71;UBERON:0004290!3.32e-19!71;UBERON:0009618!3.32e-19!71;UBERON:0003077!1.12e-18!72;UBERON:0007285!1.12e-18!72;UBERON:0007503!7.65e-16!78;UBERON:0000486!1.57e-15!83;UBERON:0003104!5.02e-12!160;UBERON:0009142!5.02e-12!160;UBERON:0005256!1.95e-11!122;UBERON:0000948!2.90e-09!24;UBERON:0005498!2.90e-09!24;UBERON:0004140!2.90e-09!24;UBERON:0009881!2.90e-09!24;UBERON:0004141!2.90e-09!24;UBERON:0003084!2.90e-09!24;UBERON:0007005!2.90e-09!24;UBERON:0004139!2.90e-09!24;UBERON:0004291!2.90e-09!24;UBERON:0004872!1.80e-08!83;UBERON:0001637!1.16e-07!42;UBERON:0003509!1.16e-07!42;UBERON:0004572!1.16e-07!42;UBERON:0007100!1.52e-07!27;UBERON:0000475!4.93e-07!264;UBERON:0002100!5.74e-07!199;UBERON:0000926!5.75e-07!315;UBERON:0004120!5.75e-07!315;UBERON:0006603!5.75e-07!315;UBERON:0004573!6.28e-07!33;UBERON:0004571!6.28e-07!33;UBERON:0000490!7.27e-07!148;UBERON:0002204!8.53e-07!167
|ontology_enrichment_uberon=UBERON:0001134!5.71e-22!62;UBERON:0002036!5.71e-22!62;UBERON:0003082!5.71e-22!62;UBERON:0002385!1.05e-20!64;UBERON:0001015!1.05e-20!64;UBERON:0000383!1.05e-20!64;UBERON:0007524!1.99e-19!73;UBERON:0002329!3.32e-19!71;UBERON:0003059!3.32e-19!71;UBERON:0007282!3.32e-19!71;UBERON:0004290!3.32e-19!71;UBERON:0009618!3.32e-19!71;UBERON:0003077!1.12e-18!72;UBERON:0007285!1.12e-18!72;UBERON:0007503!7.65e-16!78;UBERON:0000486!1.57e-15!83;UBERON:0003104!5.02e-12!160;UBERON:0009142!5.02e-12!160;UBERON:0005256!1.95e-11!122;UBERON:0000948!2.90e-09!24;UBERON:0005498!2.90e-09!24;UBERON:0004140!2.90e-09!24;UBERON:0009881!2.90e-09!24;UBERON:0004141!2.90e-09!24;UBERON:0003084!2.90e-09!24;UBERON:0007005!2.90e-09!24;UBERON:0004139!2.90e-09!24;UBERON:0004291!2.90e-09!24;UBERON:0004872!1.80e-08!83;UBERON:0001637!1.16e-07!42;UBERON:0003509!1.16e-07!42;UBERON:0004572!1.16e-07!42;UBERON:0007100!1.52e-07!27;UBERON:0000475!4.93e-07!264;UBERON:0002100!5.74e-07!199;UBERON:0000926!5.75e-07!315;UBERON:0004120!5.75e-07!315;UBERON:0006603!5.75e-07!315;UBERON:0004573!6.28e-07!33;UBERON:0004571!6.28e-07!33;UBERON:0000490!7.27e-07!148;UBERON:0002204!8.53e-07!167
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0.259046,0.00922992,0.151046,0.142558,0.0687784,0.0584209,0.15463,0.13907,0.133591,0.00408245,0.00322239,0.0986342,0.115686,0.0981568,0.162633,0.0668707,0.0420678,0.248127,6.48619e-05,0.00157725,0.0574076,0.0401809
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.205703,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.647361,0.844289,1.79645,1.41984,1.15413,2.32461,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,1.80913,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702
}}
}}

Revision as of 15:06, 26 November 2012


Full id: C1786_diaphragm_Olfactory_Cardiac_hepatic_tridermal_umbilical_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr17:48262965..48262976,-p38@COL1A1
Hg19::chr7:94058505..94058512,+p@chr7:94058505..94058512
+
Hg19::chr7:94059695..94059708,+p@chr7:94059695..94059708
+
Hg19::chr7:94059753..94059773,+p@chr7:94059753..94059773
+
Hg19::chr7:94060167..94060180,+p@chr7:94060167..94060180
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue5.71e-2262
striated muscle tissue5.71e-2262
myotome5.71e-2262
muscle tissue1.05e-2064
musculature1.05e-2064
musculature of body1.05e-2064
dense mesenchyme tissue1.99e-1973
somite3.32e-1971
presomitic mesoderm3.32e-1971
presumptive segmental plate3.32e-1971
dermomyotome3.32e-1971
trunk paraxial mesoderm3.32e-1971
paraxial mesoderm1.12e-1872
presumptive paraxial mesoderm1.12e-1872
epithelial vesicle7.65e-1678
multilaminar epithelium1.57e-1583
mesenchyme5.02e-12160
entire embryonic mesenchyme5.02e-12160
trunk mesenchyme1.95e-11122
heart2.90e-0924
primitive heart tube2.90e-0924
primary heart field2.90e-0924
anterior lateral plate mesoderm2.90e-0924
heart tube2.90e-0924
heart primordium2.90e-0924
cardiac mesoderm2.90e-0924
cardiogenic plate2.90e-0924
heart rudiment2.90e-0924
splanchnic layer of lateral plate mesoderm1.80e-0883
artery1.16e-0742
arterial blood vessel1.16e-0742
arterial system1.16e-0742
primary circulatory organ1.52e-0727
organism subdivision4.93e-07264
trunk5.74e-07199
mesoderm5.75e-07315
mesoderm-derived structure5.75e-07315
presumptive mesoderm5.75e-07315
systemic artery6.28e-0733
systemic arterial system6.28e-0733
unilaminar epithelium7.27e-07148
musculoskeletal system8.53e-07167
Disease
Ontology termp-valuen
ovarian cancer1.93e-0714


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)

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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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