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Coexpression cluster:C2890: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!9.95e-11!143;DOID:305!2.47e-10!106;DOID:1749!2.77e-07!14;DOID:162!6.89e-07!235;DOID:14566!9.18e-07!239
|ontology_enrichment_disease=DOID:0050687!9.95e-11!143;DOID:305!2.47e-10!106;DOID:1749!2.77e-07!14;DOID:162!6.89e-07!235;DOID:14566!9.18e-07!239
|ontology_enrichment_uberon=UBERON:0002100!1.98e-22!216;UBERON:0003914!1.67e-20!118;UBERON:0003104!9.74e-20!238;UBERON:0009142!9.74e-20!238;UBERON:0005177!5.62e-19!107;UBERON:0009569!1.73e-16!113;UBERON:0000466!2.94e-16!126;UBERON:0000464!4.01e-15!104;UBERON:0000490!9.65e-15!138;UBERON:0005256!3.12e-14!143;UBERON:0000483!3.65e-14!309;UBERON:0003886!3.90e-14!63;UBERON:0004111!9.09e-14!241;UBERON:0001981!1.33e-13!60;UBERON:0007500!1.33e-13!60;UBERON:0004537!1.33e-13!60;UBERON:0006965!1.33e-13!60;UBERON:0000926!1.58e-13!448;UBERON:0004120!1.58e-13!448;UBERON:0006603!1.58e-13!448;UBERON:0000119!1.59e-13!312;UBERON:0000055!2.07e-13!69;UBERON:0002417!5.32e-13!61;UBERON:0000916!5.32e-13!61;UBERON:0003064!2.67e-12!37;UBERON:0000025!6.51e-12!194;UBERON:0001008!6.67e-12!45;UBERON:0004872!6.70e-12!84;UBERON:0006554!1.01e-11!44;UBERON:0000489!1.10e-11!32;UBERON:0002553!1.82e-11!70;UBERON:0005172!2.37e-11!55;UBERON:0005173!2.37e-11!55;UBERON:0004921!9.99e-11!129;UBERON:0004185!9.99e-11!129;UBERON:0001637!1.18e-10!42;UBERON:0003509!1.18e-10!42;UBERON:0004572!1.18e-10!42;UBERON:0000481!2.30e-10!347;UBERON:0002113!4.43e-10!27;UBERON:0003918!4.43e-10!27;UBERON:0005095!4.43e-10!27;UBERON:0007687!4.43e-10!27;UBERON:0002049!4.44e-10!79;UBERON:0007798!4.44e-10!79;UBERON:0000477!1.11e-09!286;UBERON:0006555!1.22e-09!17;UBERON:0005103!1.22e-09!17;UBERON:0000083!1.22e-09!17;UBERON:0009201!1.22e-09!17;UBERON:0004819!1.22e-09!17;UBERON:0006553!1.22e-09!17;UBERON:0003074!1.22e-09!17;UBERON:0003060!1.22e-09!17;UBERON:0003103!1.24e-09!69;UBERON:0004211!1.51e-09!16;UBERON:0001285!1.51e-09!16;UBERON:0007684!1.51e-09!16;UBERON:0003220!1.51e-09!16;UBERON:0004208!1.51e-09!16;UBERON:0000475!1.58e-09!365;UBERON:0000080!1.94e-09!18;UBERON:0002120!1.94e-09!18;UBERON:0004875!1.94e-09!18;UBERON:0005721!1.94e-09!18;UBERON:0005754!1.94e-09!18;UBERON:0007297!1.94e-09!18;UBERON:0000077!5.72e-09!130;UBERON:0003887!9.20e-09!21;UBERON:0001851!1.01e-08!16;UBERON:0001007!1.24e-08!155;UBERON:0001555!1.24e-08!155;UBERON:0007026!1.24e-08!155;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0001134!2.00e-08!61;UBERON:0002036!2.00e-08!61;UBERON:0003082!2.00e-08!61;UBERON:0009773!2.45e-08!12;UBERON:0001231!2.45e-08!12;UBERON:0004810!2.45e-08!12;UBERON:0004119!2.70e-08!169;UBERON:0000925!2.70e-08!169;UBERON:0006595!2.70e-08!169;UBERON:0004573!2.80e-08!33;UBERON:0004571!2.80e-08!33;UBERON:0000058!4.17e-08!26;UBERON:0004876!9.51e-08!20;UBERON:0000922!1.01e-07!612;UBERON:0000923!1.11e-07!604;UBERON:0005291!1.11e-07!604;UBERON:0006598!1.11e-07!604;UBERON:0002532!1.11e-07!604;UBERON:0002050!1.50e-07!605;UBERON:0005423!1.50e-07!605;UBERON:0000353!2.28e-07!17;UBERON:0001225!2.48e-07!13;UBERON:0008987!2.48e-07!13;UBERON:0000468!2.70e-07!659;UBERON:0005911!2.97e-07!82;UBERON:0002323!3.36e-07!46;UBERON:0004458!7.29e-07!49
|ontology_enrichment_uberon=UBERON:0002100!1.98e-22!216;UBERON:0003914!1.67e-20!118;UBERON:0003104!9.74e-20!238;UBERON:0009142!9.74e-20!238;UBERON:0005177!5.62e-19!107;UBERON:0009569!1.73e-16!113;UBERON:0000466!2.94e-16!126;UBERON:0000464!4.01e-15!104;UBERON:0000490!9.65e-15!138;UBERON:0005256!3.12e-14!143;UBERON:0000483!3.65e-14!309;UBERON:0003886!3.90e-14!63;UBERON:0004111!9.09e-14!241;UBERON:0001981!1.33e-13!60;UBERON:0007500!1.33e-13!60;UBERON:0004537!1.33e-13!60;UBERON:0006965!1.33e-13!60;UBERON:0000926!1.58e-13!448;UBERON:0004120!1.58e-13!448;UBERON:0006603!1.58e-13!448;UBERON:0000119!1.59e-13!312;UBERON:0000055!2.07e-13!69;UBERON:0002417!5.32e-13!61;UBERON:0000916!5.32e-13!61;UBERON:0003064!2.67e-12!37;UBERON:0000025!6.51e-12!194;UBERON:0001008!6.67e-12!45;UBERON:0004872!6.70e-12!84;UBERON:0006554!1.01e-11!44;UBERON:0000489!1.10e-11!32;UBERON:0002553!1.82e-11!70;UBERON:0005172!2.37e-11!55;UBERON:0005173!2.37e-11!55;UBERON:0004921!9.99e-11!129;UBERON:0004185!9.99e-11!129;UBERON:0001637!1.18e-10!42;UBERON:0003509!1.18e-10!42;UBERON:0004572!1.18e-10!42;UBERON:0000481!2.30e-10!347;UBERON:0002113!4.43e-10!27;UBERON:0003918!4.43e-10!27;UBERON:0005095!4.43e-10!27;UBERON:0007687!4.43e-10!27;UBERON:0002049!4.44e-10!79;UBERON:0007798!4.44e-10!79;UBERON:0000477!1.11e-09!286;UBERON:0006555!1.22e-09!17;UBERON:0005103!1.22e-09!17;UBERON:0000083!1.22e-09!17;UBERON:0009201!1.22e-09!17;UBERON:0004819!1.22e-09!17;UBERON:0006553!1.22e-09!17;UBERON:0003074!1.22e-09!17;UBERON:0003060!1.22e-09!17;UBERON:0003103!1.24e-09!69;UBERON:0004211!1.51e-09!16;UBERON:0001285!1.51e-09!16;UBERON:0007684!1.51e-09!16;UBERON:0003220!1.51e-09!16;UBERON:0004208!1.51e-09!16;UBERON:0000475!1.58e-09!365;UBERON:0000080!1.94e-09!18;UBERON:0002120!1.94e-09!18;UBERON:0004875!1.94e-09!18;UBERON:0005721!1.94e-09!18;UBERON:0005754!1.94e-09!18;UBERON:0007297!1.94e-09!18;UBERON:0000077!5.72e-09!130;UBERON:0003887!9.20e-09!21;UBERON:0001851!1.01e-08!16;UBERON:0001007!1.24e-08!155;UBERON:0001555!1.24e-08!155;UBERON:0007026!1.24e-08!155;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0001134!2.00e-08!61;UBERON:0002036!2.00e-08!61;UBERON:0003082!2.00e-08!61;UBERON:0009773!2.45e-08!12;UBERON:0001231!2.45e-08!12;UBERON:0004810!2.45e-08!12;UBERON:0004119!2.70e-08!169;UBERON:0000925!2.70e-08!169;UBERON:0006595!2.70e-08!169;UBERON:0004573!2.80e-08!33;UBERON:0004571!2.80e-08!33;UBERON:0000058!4.17e-08!26;UBERON:0004876!9.51e-08!20;UBERON:0000922!1.01e-07!612;UBERON:0000923!1.11e-07!604;UBERON:0005291!1.11e-07!604;UBERON:0006598!1.11e-07!604;UBERON:0002532!1.11e-07!604;UBERON:0002050!1.50e-07!605;UBERON:0005423!1.50e-07!605;UBERON:0000353!2.28e-07!17;UBERON:0001225!2.48e-07!13;UBERON:0008987!2.48e-07!13;UBERON:0000468!2.70e-07!659;UBERON:0005911!2.97e-07!82;UBERON:0002323!3.36e-07!46;UBERON:0004458!7.29e-07!49
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}}
}}

Revision as of 13:14, 5 September 2012


Full id: C2890_Smooth_glioma_clear_Renal_endometrial_mesothelioma_gastric



Phase1 CAGE Peaks

Hg19::chr7:27153428..27153440,-p3@HOXA3
Hg19::chr7:27153443..27153450,-p8@HOXA3
Hg19::chr7:27153454..27153469,-p2@HOXA3
Hg19::chr7:27153613..27153630,-p6@HOXA3


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
trunk1.98e-22216
epithelial tube1.67e-20118
mesenchyme9.74e-20238
entire embryonic mesenchyme9.74e-20238
trunk region element5.62e-19107
subdivision of trunk1.73e-16113
immaterial anatomical entity2.94e-16126
anatomical space4.01e-15104
unilaminar epithelium9.65e-15138
trunk mesenchyme3.12e-14143
epithelium3.65e-14309
body cavity precursor3.90e-1463
anatomical conduit9.09e-14241
blood vessel1.33e-1360
epithelial tube open at both ends1.33e-1360
blood vasculature1.33e-1360
vascular cord1.33e-1360
mesoderm1.58e-13448
mesoderm-derived structure1.58e-13448
presumptive mesoderm1.58e-13448
cell layer1.59e-13312
vessel2.07e-1369
abdominal segment of trunk5.32e-1361
abdomen5.32e-1361
intermediate mesoderm2.67e-1237
tube6.51e-12194
renal system6.67e-1245
splanchnic layer of lateral plate mesoderm6.70e-1284
urinary system structure1.01e-1144
cavitated compound organ1.10e-1132
anatomical cavity1.82e-1170
abdomen element2.37e-1155
abdominal segment element2.37e-1155
subdivision of digestive tract9.99e-11129
endodermal part of digestive tract9.99e-11129
artery1.18e-1042
arterial blood vessel1.18e-1042
arterial system1.18e-1042
multi-tissue structure2.30e-10347
kidney4.43e-1027
kidney mesenchyme4.43e-1027
kidney rudiment4.43e-1027
kidney field4.43e-1027
vasculature4.44e-1079
vascular system4.44e-1079
anatomical cluster1.11e-09286
excretory tube1.22e-0917
mesonephric epithelium1.22e-0917
mesonephric tubule1.22e-0917
nephric duct1.22e-0917
kidney epithelium1.22e-0917
renal duct1.22e-0917
mesonephric duct1.22e-0917
pronephric duct1.22e-0917
compound organ1.24e-0969
nephron epithelium1.51e-0916
nephron1.51e-0916
uriniferous tubule1.51e-0916
metanephric mesenchyme1.51e-0916
nephrogenic mesenchyme1.51e-0916
organism subdivision1.58e-09365
mesonephros1.94e-0918
pronephros1.94e-0918
nephrogenic cord1.94e-0918
pronephric mesoderm1.94e-0918
rostral part of nephrogenic cord1.94e-0918
presumptive pronephric mesoderm1.94e-0918
mixed endoderm/mesoderm-derived structure5.72e-09130
intraembryonic coelom9.20e-0921
cortex1.01e-0816
digestive system1.24e-08155
digestive tract1.24e-08155
primitive gut1.24e-08155
muscle tissue1.29e-0863
musculature1.29e-0863
musculature of body1.29e-0863

Disease
Ontology termp-valuen


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488347.03775025449611.60047699357395e-050.000370543597277477
RFX5#5993412.04791082719514.74457429336527e-050.00082876500188121



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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