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Coexpression cluster:C4677: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!5.12e-22!216;UBERON:0003104!3.42e-21!238;UBERON:0009142!3.42e-21!238;UBERON:0000055!6.20e-21!69;UBERON:0003914!2.60e-20!118;UBERON:0001981!1.97e-18!60;UBERON:0007500!1.97e-18!60;UBERON:0004537!1.97e-18!60;UBERON:0006965!1.97e-18!60;UBERON:0000490!2.44e-18!138;UBERON:0005256!7.13e-17!143;UBERON:0002049!9.77e-16!79;UBERON:0007798!9.77e-16!79;UBERON:0000926!1.16e-14!448;UBERON:0004120!1.16e-14!448;UBERON:0006603!1.16e-14!448;UBERON:0004872!1.27e-14!84;UBERON:0005177!5.37e-14!107;UBERON:0002385!2.37e-13!63;UBERON:0001015!2.37e-13!63;UBERON:0000383!2.37e-13!63;UBERON:0004111!8.35e-13!241;UBERON:0001134!1.00e-12!61;UBERON:0002036!1.00e-12!61;UBERON:0003082!1.00e-12!61;UBERON:0001637!1.79e-12!42;UBERON:0003509!1.79e-12!42;UBERON:0004572!1.79e-12!42;UBERON:0003064!4.77e-12!37;UBERON:0009569!1.79e-11!113;UBERON:0000466!2.33e-11!126;UBERON:0004921!5.86e-11!129;UBERON:0004185!5.86e-11!129;UBERON:0000464!9.41e-11!104;UBERON:0003886!1.09e-10!63;UBERON:0004290!3.47e-10!70;UBERON:0000481!3.68e-10!347;UBERON:0001008!9.63e-10!45;UBERON:0000477!9.94e-10!286;UBERON:0000483!1.46e-09!309;UBERON:0001986!1.48e-09!18;UBERON:0004638!1.48e-09!18;UBERON:0004852!1.48e-09!18;UBERON:0004573!1.93e-09!33;UBERON:0004571!1.93e-09!33;UBERON:0006554!3.20e-09!44;UBERON:0002553!3.92e-09!70;UBERON:0000119!4.93e-09!312;UBERON:0000025!6.16e-09!194;UBERON:0000487!9.39e-09!22;UBERON:0001009!1.33e-08!113;UBERON:0002417!1.44e-08!61;UBERON:0000916!1.44e-08!61;UBERON:0000947!1.83e-08!21;UBERON:0010191!1.83e-08!21;UBERON:0004535!1.95e-08!110;UBERON:0001007!2.66e-08!155;UBERON:0001555!2.66e-08!155;UBERON:0007026!2.66e-08!155;UBERON:0000489!2.70e-08!32;UBERON:0005172!4.15e-08!55;UBERON:0005173!4.15e-08!55;UBERON:0005156!7.39e-08!59;UBERON:0000990!7.39e-08!59;UBERON:0000486!9.29e-08!82;UBERON:0000077!1.11e-07!130;UBERON:0004119!2.04e-07!169;UBERON:0000925!2.04e-07!169;UBERON:0006595!2.04e-07!169;UBERON:0006914!3.04e-07!25;UBERON:0000475!4.62e-07!365;UBERON:0005409!5.33e-07!35;UBERON:0000080!7.29e-07!18;UBERON:0002120!7.29e-07!18;UBERON:0004875!7.29e-07!18;UBERON:0005721!7.29e-07!18;UBERON:0005754!7.29e-07!18;UBERON:0007297!7.29e-07!18;UBERON:0000914!7.37e-07!83;UBERON:0002329!7.37e-07!83;UBERON:0003077!7.37e-07!83;UBERON:0003059!7.37e-07!83;UBERON:0007282!7.37e-07!83;UBERON:0009618!7.37e-07!83;UBERON:0007285!7.37e-07!83;UBERON:0002113!8.46e-07!27;UBERON:0003918!8.46e-07!27;UBERON:0005095!8.46e-07!27;UBERON:0007687!8.46e-07!27
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}}
}}

Revision as of 20:14, 8 August 2012


Full id: C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial



Phase1 CAGE Peaks

Hg19::chr7:27153185..27153215,+p1@ENST00000522193
Hg19::chr7:27153226..27153257,+p2@ENST00000522193
Hg19::chr7:27153269..27153285,+p3@ENST00000522193


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
trunk5.12e-22216
mesenchyme3.42e-21238
entire embryonic mesenchyme3.42e-21238
vessel6.20e-2169
epithelial tube2.60e-20118
blood vessel1.97e-1860
epithelial tube open at both ends1.97e-1860
blood vasculature1.97e-1860
vascular cord1.97e-1860
unilaminar epithelium2.44e-18138
trunk mesenchyme7.13e-17143
vasculature9.77e-1679
vascular system9.77e-1679
mesoderm1.16e-14448
mesoderm-derived structure1.16e-14448
presumptive mesoderm1.16e-14448
splanchnic layer of lateral plate mesoderm1.27e-1484
trunk region element5.37e-14107
muscle tissue2.37e-1363
musculature2.37e-1363
musculature of body2.37e-1363
anatomical conduit8.35e-13241
skeletal muscle tissue1.00e-1261
striated muscle tissue1.00e-1261
myotome1.00e-1261
artery1.79e-1242
arterial blood vessel1.79e-1242
arterial system1.79e-1242
intermediate mesoderm4.77e-1237
subdivision of trunk1.79e-11113
immaterial anatomical entity2.33e-11126
subdivision of digestive tract5.86e-11129
endodermal part of digestive tract5.86e-11129
anatomical space9.41e-11104
body cavity precursor1.09e-1063
dermomyotome3.47e-1070
multi-tissue structure3.68e-10347
renal system9.63e-1045
anatomical cluster9.94e-10286
epithelium1.46e-09309
endothelium1.48e-0918
blood vessel endothelium1.48e-0918
cardiovascular system endothelium1.48e-0918
systemic artery1.93e-0933
systemic arterial system1.93e-0933
urinary system structure3.20e-0944
anatomical cavity3.92e-0970
cell layer4.93e-09312
tube6.16e-09194
simple squamous epithelium9.39e-0922
circulatory system1.33e-08113
abdominal segment of trunk1.44e-0861
abdomen1.44e-0861
aorta1.83e-0821
aortic system1.83e-0821
cardiovascular system1.95e-08110
digestive system2.66e-08155
digestive tract2.66e-08155
primitive gut2.66e-08155
cavitated compound organ2.70e-0832
abdomen element4.15e-0855
abdominal segment element4.15e-0855
reproductive structure7.39e-0859
reproductive system7.39e-0859
multilaminar epithelium9.29e-0882
mixed endoderm/mesoderm-derived structure1.11e-07130
endoderm-derived structure2.04e-07169
endoderm2.04e-07169
presumptive endoderm2.04e-07169
squamous epithelium3.04e-0725
organism subdivision4.62e-07365
gastrointestinal system5.33e-0735
mesonephros7.29e-0718
pronephros7.29e-0718
nephrogenic cord7.29e-0718
pronephric mesoderm7.29e-0718
rostral part of nephrogenic cord7.29e-0718
presumptive pronephric mesoderm7.29e-0718


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.