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Coexpression cluster:C2672: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004876!6.65e-16!20;UBERON:0000080!2.25e-13!18;UBERON:0002120!2.25e-13!18;UBERON:0004875!2.25e-13!18;UBERON:0005721!2.25e-13!18;UBERON:0005754!2.25e-13!18;UBERON:0007297!2.25e-13!18;UBERON:0003887!2.65e-12!21;UBERON:0000489!3.59e-12!32;UBERON:0006555!3.63e-12!17;UBERON:0005103!3.63e-12!17;UBERON:0000083!3.63e-12!17;UBERON:0009201!3.63e-12!17;UBERON:0004819!3.63e-12!17;UBERON:0006553!3.63e-12!17;UBERON:0003074!3.63e-12!17;UBERON:0003060!3.63e-12!17;UBERON:0002113!5.73e-12!27;UBERON:0003918!5.73e-12!27;UBERON:0005095!5.73e-12!27;UBERON:0007687!5.73e-12!27;UBERON:0004211!4.98e-11!16;UBERON:0001285!4.98e-11!16;UBERON:0007684!4.98e-11!16;UBERON:0003220!4.98e-11!16;UBERON:0004208!4.98e-11!16;UBERON:0000058!5.59e-11!26;UBERON:0009773!5.94e-11!12;UBERON:0001231!5.94e-11!12;UBERON:0004810!5.94e-11!12;UBERON:0003133!1.50e-10!48;UBERON:0003064!8.33e-10!37;UBERON:0003886!1.40e-09!63;UBERON:0003135!2.27e-09!11;UBERON:0001473!2.58e-09!8;UBERON:0004536!2.58e-09!8;UBERON:0006558!2.58e-09!8;UBERON:0002465!3.33e-09!10;UBERON:0002553!1.28e-08!70;UBERON:0005156!2.84e-08!59;UBERON:0000990!2.84e-08!59;UBERON:0003103!3.39e-08!69;UBERON:0000464!4.55e-08!104;UBERON:0001008!4.94e-08!45;UBERON:0001225!1.08e-07!13;UBERON:0008987!1.08e-07!13;UBERON:0006554!2.37e-07!44;UBERON:0005631!3.93e-07!14;UBERON:0000158!3.93e-07!14
|ontology_enrichment_uberon=UBERON:0004876!6.65e-16!20;UBERON:0000080!2.25e-13!18;UBERON:0002120!2.25e-13!18;UBERON:0004875!2.25e-13!18;UBERON:0005721!2.25e-13!18;UBERON:0005754!2.25e-13!18;UBERON:0007297!2.25e-13!18;UBERON:0003887!2.65e-12!21;UBERON:0000489!3.59e-12!32;UBERON:0006555!3.63e-12!17;UBERON:0005103!3.63e-12!17;UBERON:0000083!3.63e-12!17;UBERON:0009201!3.63e-12!17;UBERON:0004819!3.63e-12!17;UBERON:0006553!3.63e-12!17;UBERON:0003074!3.63e-12!17;UBERON:0003060!3.63e-12!17;UBERON:0002113!5.73e-12!27;UBERON:0003918!5.73e-12!27;UBERON:0005095!5.73e-12!27;UBERON:0007687!5.73e-12!27;UBERON:0004211!4.98e-11!16;UBERON:0001285!4.98e-11!16;UBERON:0007684!4.98e-11!16;UBERON:0003220!4.98e-11!16;UBERON:0004208!4.98e-11!16;UBERON:0000058!5.59e-11!26;UBERON:0009773!5.94e-11!12;UBERON:0001231!5.94e-11!12;UBERON:0004810!5.94e-11!12;UBERON:0003133!1.50e-10!48;UBERON:0003064!8.33e-10!37;UBERON:0003886!1.40e-09!63;UBERON:0003135!2.27e-09!11;UBERON:0001473!2.58e-09!8;UBERON:0004536!2.58e-09!8;UBERON:0006558!2.58e-09!8;UBERON:0002465!3.33e-09!10;UBERON:0002553!1.28e-08!70;UBERON:0005156!2.84e-08!59;UBERON:0000990!2.84e-08!59;UBERON:0003103!3.39e-08!69;UBERON:0000464!4.55e-08!104;UBERON:0001008!4.94e-08!45;UBERON:0001225!1.08e-07!13;UBERON:0008987!1.08e-07!13;UBERON:0006554!2.37e-07!44;UBERON:0005631!3.93e-07!14;UBERON:0000158!3.93e-07!14
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}}
}}

Revision as of 18:30, 8 August 2012


Full id: C2672_uterus_kidney_nonsmall_smallcell_breast_Osteoblast_Endothelial



Phase1 CAGE Peaks

Hg19::chr2:176981499..176981522,+p2@HOXD10
Hg19::chr2:176981526..176981543,+p3@HOXD10
Hg19::chr2:176981546..176981557,+p5@HOXD10
Hg19::chr2:176985956..176985979,+p@chr2:176985956..176985979
+


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
urogenital ridge6.65e-1620
mesonephros2.25e-1318
pronephros2.25e-1318
nephrogenic cord2.25e-1318
pronephric mesoderm2.25e-1318
rostral part of nephrogenic cord2.25e-1318
presumptive pronephric mesoderm2.25e-1318
intraembryonic coelom2.65e-1221
cavitated compound organ3.59e-1232
excretory tube3.63e-1217
mesonephric epithelium3.63e-1217
mesonephric tubule3.63e-1217
nephric duct3.63e-1217
kidney epithelium3.63e-1217
renal duct3.63e-1217
mesonephric duct3.63e-1217
pronephric duct3.63e-1217
kidney5.73e-1227
kidney mesenchyme5.73e-1227
kidney rudiment5.73e-1227
kidney field5.73e-1227
nephron epithelium4.98e-1116
nephron4.98e-1116
uriniferous tubule4.98e-1116
metanephric mesenchyme4.98e-1116
nephrogenic mesenchyme4.98e-1116
duct5.59e-1126
renal tubule5.94e-1112
nephron tubule5.94e-1112
nephron tubule epithelium5.94e-1112
reproductive organ1.50e-1048
intermediate mesoderm8.33e-1037
body cavity precursor1.40e-0963
male reproductive organ2.27e-0911
lymphatic vessel2.58e-098
lymph vasculature2.58e-098
lymphatic part of lymphoid system2.58e-098
lymphoid system3.33e-0910
anatomical cavity1.28e-0870
reproductive structure2.84e-0859
reproductive system2.84e-0859
compound organ3.39e-0869
anatomical space4.55e-08104
renal system4.94e-0845
cortex of kidney1.08e-0713
renal parenchyma1.08e-0713
urinary system structure2.37e-0744
extraembryonic membrane3.93e-0714
membranous layer3.93e-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)

{{{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

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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