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Coexpression cluster:C1917: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0006554!2.42e-18!44;UBERON:0000489!7.60e-18!32;UBERON:0001008!8.88e-18!45;UBERON:0002113!5.57e-16!27;UBERON:0003918!5.57e-16!27;UBERON:0005095!5.57e-16!27;UBERON:0007687!5.57e-16!27;UBERON:0005172!3.08e-13!55;UBERON:0005173!3.08e-13!55;UBERON:0009773!8.72e-13!12;UBERON:0001231!8.72e-13!12;UBERON:0004810!8.72e-13!12;UBERON:0000080!5.63e-12!18;UBERON:0002120!5.63e-12!18;UBERON:0004875!5.63e-12!18;UBERON:0005721!5.63e-12!18;UBERON:0005754!5.63e-12!18;UBERON:0007297!5.63e-12!18;UBERON:0003887!7.47e-12!21;UBERON:0002417!2.74e-11!61;UBERON:0000916!2.74e-11!61;UBERON:0006555!1.44e-10!17;UBERON:0005103!1.44e-10!17;UBERON:0000083!1.44e-10!17;UBERON:0009201!1.44e-10!17;UBERON:0004819!1.44e-10!17;UBERON:0006553!1.44e-10!17;UBERON:0003074!1.44e-10!17;UBERON:0003060!1.44e-10!17;UBERON:0004876!1.72e-10!20;UBERON:0000058!1.83e-10!26;UBERON:0003135!2.25e-10!11;UBERON:0005156!3.46e-09!59;UBERON:0000990!3.46e-09!59;UBERON:0004211!4.71e-09!16;UBERON:0001285!4.71e-09!16;UBERON:0007684!4.71e-09!16;UBERON:0003220!4.71e-09!16;UBERON:0004208!4.71e-09!16;UBERON:0007023!6.52e-09!115;UBERON:0003133!9.85e-09!48;UBERON:0003064!1.15e-08!37;UBERON:0003101!1.42e-08!22;UBERON:0000079!1.42e-08!22;UBERON:0003886!2.85e-08!63;UBERON:0005177!4.71e-08!107;UBERON:0000473!5.25e-08!8;UBERON:0004175!1.78e-07!25;UBERON:0006947!2.31e-07!3;UBERON:0004054!2.31e-07!3;UBERON:0006853!3.90e-07!3;UBERON:0007685!3.90e-07!3;UBERON:0004134!3.90e-07!3;UBERON:0002553!6.44e-07!70;UBERON:0001225!7.12e-07!13;UBERON:0008987!7.12e-07!13
|ontology_enrichment_uberon=UBERON:0006554!2.42e-18!44;UBERON:0000489!7.60e-18!32;UBERON:0001008!8.88e-18!45;UBERON:0002113!5.57e-16!27;UBERON:0003918!5.57e-16!27;UBERON:0005095!5.57e-16!27;UBERON:0007687!5.57e-16!27;UBERON:0005172!3.08e-13!55;UBERON:0005173!3.08e-13!55;UBERON:0009773!8.72e-13!12;UBERON:0001231!8.72e-13!12;UBERON:0004810!8.72e-13!12;UBERON:0000080!5.63e-12!18;UBERON:0002120!5.63e-12!18;UBERON:0004875!5.63e-12!18;UBERON:0005721!5.63e-12!18;UBERON:0005754!5.63e-12!18;UBERON:0007297!5.63e-12!18;UBERON:0003887!7.47e-12!21;UBERON:0002417!2.74e-11!61;UBERON:0000916!2.74e-11!61;UBERON:0006555!1.44e-10!17;UBERON:0005103!1.44e-10!17;UBERON:0000083!1.44e-10!17;UBERON:0009201!1.44e-10!17;UBERON:0004819!1.44e-10!17;UBERON:0006553!1.44e-10!17;UBERON:0003074!1.44e-10!17;UBERON:0003060!1.44e-10!17;UBERON:0004876!1.72e-10!20;UBERON:0000058!1.83e-10!26;UBERON:0003135!2.25e-10!11;UBERON:0005156!3.46e-09!59;UBERON:0000990!3.46e-09!59;UBERON:0004211!4.71e-09!16;UBERON:0001285!4.71e-09!16;UBERON:0007684!4.71e-09!16;UBERON:0003220!4.71e-09!16;UBERON:0004208!4.71e-09!16;UBERON:0007023!6.52e-09!115;UBERON:0003133!9.85e-09!48;UBERON:0003064!1.15e-08!37;UBERON:0003101!1.42e-08!22;UBERON:0000079!1.42e-08!22;UBERON:0003886!2.85e-08!63;UBERON:0005177!4.71e-08!107;UBERON:0000473!5.25e-08!8;UBERON:0004175!1.78e-07!25;UBERON:0006947!2.31e-07!3;UBERON:0004054!2.31e-07!3;UBERON:0006853!3.90e-07!3;UBERON:0007685!3.90e-07!3;UBERON:0004134!3.90e-07!3;UBERON:0002553!6.44e-07!70;UBERON:0001225!7.12e-07!13;UBERON:0008987!7.12e-07!13
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}}
}}

Revision as of 17:47, 8 August 2012


Full id: C1917_clear_epididymis_serous_uterus_kidney_B_ductus



Phase1 CAGE Peaks

Hg19::chr3:112127710..112127713,-p@chr3:112127710..112127713
-
Hg19::chr3:112128019..112128034,-p1@ENST00000486726
Hg19::chr3:112128117..112128134,-p2@ENST00000486726
Hg19::chr5:138905822..138905827,+p10@UBE2D2
Hg19::chr7:76911466..76911478,+p4@CCDC146


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

GO IDGO nameFDR corrected p-value
GO:0004842ubiquitin-protein ligase activity0.033249604249251
GO:0008639small protein conjugating enzyme activity0.033249604249251
GO:0019787small conjugating protein ligase activity0.033249604249251
GO:0006511ubiquitin-dependent protein catabolic process0.033249604249251
GO:0043632modification-dependent macromolecule catabolic process0.033249604249251
GO:0019941modification-dependent protein catabolic process0.033249604249251
GO:0051603proteolysis involved in cellular protein catabolic process0.033249604249251
GO:0044257cellular protein catabolic process0.033249604249251
GO:0016881acid-amino acid ligase activity0.033249604249251
GO:0030163protein catabolic process0.0337550710210548
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0337550710210548
GO:0051246regulation of protein metabolic process0.0349518608084486
GO:0043285biopolymer catabolic process0.0349518608084486
GO:0044265cellular macromolecule catabolic process0.0366301660190745
GO:0006512ubiquitin cycle0.0366301660190745
GO:0009057macromolecule catabolic process0.0380901919227599
GO:0016874ligase activity0.0380901919227599
GO:0044248cellular catabolic process0.0449814880228161



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
urinary system structure2.42e-1844
cavitated compound organ7.60e-1832
renal system8.88e-1845
kidney5.57e-1627
kidney mesenchyme5.57e-1627
kidney rudiment5.57e-1627
kidney field5.57e-1627
abdomen element3.08e-1355
abdominal segment element3.08e-1355
renal tubule8.72e-1312
nephron tubule8.72e-1312
nephron tubule epithelium8.72e-1312
mesonephros5.63e-1218
pronephros5.63e-1218
nephrogenic cord5.63e-1218
pronephric mesoderm5.63e-1218
rostral part of nephrogenic cord5.63e-1218
presumptive pronephric mesoderm5.63e-1218
intraembryonic coelom7.47e-1221
abdominal segment of trunk2.74e-1161
abdomen2.74e-1161
excretory tube1.44e-1017
mesonephric epithelium1.44e-1017
mesonephric tubule1.44e-1017
nephric duct1.44e-1017
kidney epithelium1.44e-1017
renal duct1.44e-1017
mesonephric duct1.44e-1017
pronephric duct1.44e-1017
urogenital ridge1.72e-1020
duct1.83e-1026
male reproductive organ2.25e-1011
reproductive structure3.46e-0959
reproductive system3.46e-0959
nephron epithelium4.71e-0916
nephron4.71e-0916
uriniferous tubule4.71e-0916
metanephric mesenchyme4.71e-0916
nephrogenic mesenchyme4.71e-0916
adult organism6.52e-09115
reproductive organ9.85e-0948
intermediate mesoderm1.15e-0837
male organism1.42e-0822
male reproductive system1.42e-0822
body cavity precursor2.85e-0863
trunk region element4.71e-08107
testis5.25e-088
internal genitalia1.78e-0725
male genital duct2.31e-073
internal male genitalia2.31e-073
renal cortex tubule3.90e-073
region of nephron tubule3.90e-073
proximal tubule3.90e-073
anatomical cavity6.44e-0770
cortex of kidney7.12e-0713
renal parenchyma7.12e-0713


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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