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Coexpression cluster:C3645: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!2.32e-19!216;UBERON:0000489!6.61e-17!32;UBERON:0002113!1.17e-14!27;UBERON:0003918!1.17e-14!27;UBERON:0005095!1.17e-14!27;UBERON:0007687!1.17e-14!27;UBERON:0000080!3.78e-14!18;UBERON:0002120!3.78e-14!18;UBERON:0004875!3.78e-14!18;UBERON:0005721!3.78e-14!18;UBERON:0005754!3.78e-14!18;UBERON:0007297!3.78e-14!18;UBERON:0005256!1.87e-13!143;UBERON:0006555!2.47e-13!17;UBERON:0005103!2.47e-13!17;UBERON:0000083!2.47e-13!17;UBERON:0009201!2.47e-13!17;UBERON:0004819!2.47e-13!17;UBERON:0006553!2.47e-13!17;UBERON:0003074!2.47e-13!17;UBERON:0003060!2.47e-13!17;UBERON:0000058!2.78e-13!26;UBERON:0003914!3.07e-13!118;UBERON:0003887!3.21e-13!21;UBERON:0002417!3.64e-13!61;UBERON:0000916!3.64e-13!61;UBERON:0005177!5.02e-13!107;UBERON:0003104!5.20e-13!238;UBERON:0009142!5.20e-13!238;UBERON:0004211!1.37e-12!16;UBERON:0001285!1.37e-12!16;UBERON:0007684!1.37e-12!16;UBERON:0003220!1.37e-12!16;UBERON:0004208!1.37e-12!16;UBERON:0001008!1.76e-12!45;UBERON:0009569!2.34e-12!113;UBERON:0006554!3.93e-12!44;UBERON:0004876!9.17e-12!20;UBERON:0000353!1.71e-11!17;UBERON:0005172!5.52e-11!55;UBERON:0005173!5.52e-11!55;UBERON:0001225!9.87e-11!13;UBERON:0008987!9.87e-11!13;UBERON:0009773!9.37e-10!12;UBERON:0001231!9.37e-10!12;UBERON:0004810!9.37e-10!12;UBERON:0003886!1.56e-09!63;UBERON:0000466!4.67e-09!126;UBERON:0000055!5.56e-09!69;UBERON:0001851!2.23e-08!16;UBERON:0000926!2.47e-08!448;UBERON:0004120!2.47e-08!448;UBERON:0006603!2.47e-08!448;UBERON:0003064!5.92e-08!37;UBERON:0004290!6.15e-08!70;UBERON:0000486!8.19e-08!82;UBERON:0000490!9.09e-08!138;UBERON:0000464!1.02e-07!104;UBERON:0003103!2.37e-07!69;UBERON:0002553!4.65e-07!70;UBERON:0002049!6.72e-07!79;UBERON:0007798!6.72e-07!79;UBERON:0000483!9.36e-07!309
|ontology_enrichment_uberon=UBERON:0002100!2.32e-19!216;UBERON:0000489!6.61e-17!32;UBERON:0002113!1.17e-14!27;UBERON:0003918!1.17e-14!27;UBERON:0005095!1.17e-14!27;UBERON:0007687!1.17e-14!27;UBERON:0000080!3.78e-14!18;UBERON:0002120!3.78e-14!18;UBERON:0004875!3.78e-14!18;UBERON:0005721!3.78e-14!18;UBERON:0005754!3.78e-14!18;UBERON:0007297!3.78e-14!18;UBERON:0005256!1.87e-13!143;UBERON:0006555!2.47e-13!17;UBERON:0005103!2.47e-13!17;UBERON:0000083!2.47e-13!17;UBERON:0009201!2.47e-13!17;UBERON:0004819!2.47e-13!17;UBERON:0006553!2.47e-13!17;UBERON:0003074!2.47e-13!17;UBERON:0003060!2.47e-13!17;UBERON:0000058!2.78e-13!26;UBERON:0003914!3.07e-13!118;UBERON:0003887!3.21e-13!21;UBERON:0002417!3.64e-13!61;UBERON:0000916!3.64e-13!61;UBERON:0005177!5.02e-13!107;UBERON:0003104!5.20e-13!238;UBERON:0009142!5.20e-13!238;UBERON:0004211!1.37e-12!16;UBERON:0001285!1.37e-12!16;UBERON:0007684!1.37e-12!16;UBERON:0003220!1.37e-12!16;UBERON:0004208!1.37e-12!16;UBERON:0001008!1.76e-12!45;UBERON:0009569!2.34e-12!113;UBERON:0006554!3.93e-12!44;UBERON:0004876!9.17e-12!20;UBERON:0000353!1.71e-11!17;UBERON:0005172!5.52e-11!55;UBERON:0005173!5.52e-11!55;UBERON:0001225!9.87e-11!13;UBERON:0008987!9.87e-11!13;UBERON:0009773!9.37e-10!12;UBERON:0001231!9.37e-10!12;UBERON:0004810!9.37e-10!12;UBERON:0003886!1.56e-09!63;UBERON:0000466!4.67e-09!126;UBERON:0000055!5.56e-09!69;UBERON:0001851!2.23e-08!16;UBERON:0000926!2.47e-08!448;UBERON:0004120!2.47e-08!448;UBERON:0006603!2.47e-08!448;UBERON:0003064!5.92e-08!37;UBERON:0004290!6.15e-08!70;UBERON:0000486!8.19e-08!82;UBERON:0000490!9.09e-08!138;UBERON:0000464!1.02e-07!104;UBERON:0003103!2.37e-07!69;UBERON:0002553!4.65e-07!70;UBERON:0002049!6.72e-07!79;UBERON:0007798!6.72e-07!79;UBERON:0000483!9.36e-07!309
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324909677052739!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222033537464336!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196950524101374
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}}
}}

Revision as of 12:38, 5 September 2012


Full id: C3645_ductus_seminal_alveolar_endometrial_Smooth_small_nonsmall



Phase1 CAGE Peaks

Hg19::chr17:46675539..46675551,-p7@HOXB6
Hg19::chr17:46675558..46675577,-p2@HOXB6
Hg19::chr17:46675586..46675600,-p6@HOXB6


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><br>

Uber Anatomy
Ontology termp-valuen
trunk2.32e-19216
cavitated compound organ6.61e-1732
kidney1.17e-1427
kidney mesenchyme1.17e-1427
kidney rudiment1.17e-1427
kidney field1.17e-1427
mesonephros3.78e-1418
pronephros3.78e-1418
nephrogenic cord3.78e-1418
pronephric mesoderm3.78e-1418
rostral part of nephrogenic cord3.78e-1418
presumptive pronephric mesoderm3.78e-1418
trunk mesenchyme1.87e-13143
excretory tube2.47e-1317
mesonephric epithelium2.47e-1317
mesonephric tubule2.47e-1317
nephric duct2.47e-1317
kidney epithelium2.47e-1317
renal duct2.47e-1317
mesonephric duct2.47e-1317
pronephric duct2.47e-1317
duct2.78e-1326
epithelial tube3.07e-13118
intraembryonic coelom3.21e-1321
abdominal segment of trunk3.64e-1361
abdomen3.64e-1361
trunk region element5.02e-13107
mesenchyme5.20e-13238
entire embryonic mesenchyme5.20e-13238
nephron epithelium1.37e-1216
nephron1.37e-1216
uriniferous tubule1.37e-1216
metanephric mesenchyme1.37e-1216
nephrogenic mesenchyme1.37e-1216
renal system1.76e-1245
subdivision of trunk2.34e-12113
urinary system structure3.93e-1244
urogenital ridge9.17e-1220
parenchyma1.71e-1117
abdomen element5.52e-1155
abdominal segment element5.52e-1155
cortex of kidney9.87e-1113
renal parenchyma9.87e-1113
renal tubule9.37e-1012
nephron tubule9.37e-1012
nephron tubule epithelium9.37e-1012
body cavity precursor1.56e-0963
immaterial anatomical entity4.67e-09126
vessel5.56e-0969
cortex2.23e-0816
mesoderm2.47e-08448
mesoderm-derived structure2.47e-08448
presumptive mesoderm2.47e-08448
intermediate mesoderm5.92e-0837
dermomyotome6.15e-0870
multilaminar epithelium8.19e-0882
unilaminar epithelium9.09e-08138
anatomical space1.02e-07104
compound organ2.37e-0769
anatomical cavity4.65e-0770
vasculature6.72e-0779
vascular system6.72e-0779
epithelium9.36e-07309


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)

{{{tfbs_overrepresentation_jaspar}}}



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
E2F1#186934.907389214879320.008460985347239390.0324909677052739
SUZ12#23512350.11578091106297.93834897779404e-060.000222033537464336
TRIM28#10155318.59052504526250.0001555969297255280.00196950524101374



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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