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|full_id=C3135_Hepatocyte_ductus_serous_liver_seminal_kidney_epididymis
|full_id=C3135_Hepatocyte_ductus_serous_liver_seminal_kidney_epididymis
|id=C3135
|id=C3135
|ontology_enrichment_celltype=CL:0000239!4.08e-07!3;CL:1000615!4.08e-07!3;CL:0002306!4.08e-07!3;CL:0000181!8.30e-07!12;CL:0000417!8.30e-07!12;CL:0000668!8.30e-07!12;CL:0000414!8.30e-07!12;CL:0000412!8.30e-07!12;CL:0000182!8.30e-07!12
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!2.90e-16!55;UBERON:0005173!2.90e-16!55;UBERON:0005177!3.29e-16!107;UBERON:0006947!6.52e-16!3;UBERON:0004054!6.52e-16!3;UBERON:0000466!1.98e-14!126;UBERON:0002417!2.47e-14!61;UBERON:0000916!2.47e-14!61;UBERON:0009569!4.68e-12!113;UBERON:0005904!4.74e-12!4;UBERON:0009497!3.46e-11!25;UBERON:0000015!3.46e-11!25;UBERON:0002423!3.46e-11!25;UBERON:0006235!3.46e-11!25;UBERON:0004161!3.46e-11!25;UBERON:0004175!5.43e-11!25;UBERON:0001008!1.46e-10!45;UBERON:0000489!1.79e-10!32;UBERON:0002113!4.23e-10!27;UBERON:0003918!4.23e-10!27;UBERON:0005095!4.23e-10!27;UBERON:0007687!4.23e-10!27;UBERON:0008835!5.17e-10!22;UBERON:0003894!5.17e-10!22;UBERON:0003133!8.67e-10!48;UBERON:0009854!1.55e-09!23;UBERON:0005156!3.99e-09!59;UBERON:0000990!3.99e-09!59;UBERON:0007023!4.33e-09!115;UBERON:0006554!6.06e-09!44;UBERON:0002107!9.86e-09!19;UBERON:0006925!9.86e-09!19;UBERON:0008836!9.86e-09!19;UBERON:0007499!1.08e-08!25;UBERON:0000077!1.15e-08!130;UBERON:0009856!2.54e-08!26;UBERON:0005911!3.01e-08!82;UBERON:0000058!3.44e-08!26;UBERON:0002100!5.60e-08!216;UBERON:0000464!7.38e-08!104;UBERON:0004921!1.22e-07!129;UBERON:0004185!1.22e-07!129;UBERON:0003104!1.55e-07!238;UBERON:0009142!1.55e-07!238;UBERON:0003135!2.74e-07!11;UBERON:0006853!4.08e-07!3;UBERON:0007685!4.08e-07!3;UBERON:0004134!4.08e-07!3;UBERON:0003929!4.89e-07!54;UBERON:0003064!6.22e-07!37;UBERON:0003886!6.73e-07!63
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Revision as of 14:32, 21 May 2012


Full id: C3135_Hepatocyte_ductus_serous_liver_seminal_kidney_epididymis



Phase1 CAGE Peaks

Hg19::chr11:2397418..2397443,+p6@CD81
Hg19::chr11:2397485..2397493,+p22@CD81
Hg19::chr11:2397520..2397532,+p18@CD81


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>


Cell Type
Ontology termp-valuen
brush border epithelial cell4.08e-073
kidney cortex tubule cell4.08e-073
epithelial cell of proximal tubule4.08e-073
metabolising cell8.30e-0712
endopolyploid cell8.30e-0712
parenchymal cell8.30e-0712
polyploid cell8.30e-0712
hepatocyte8.30e-0712
Uber Anatomy
Ontology termp-valuen
abdomen element2.90e-1655
abdominal segment element2.90e-1655
trunk region element3.29e-16107
male genital duct6.52e-163
internal male genitalia6.52e-163
immaterial anatomical entity1.98e-14126
abdominal segment of trunk2.47e-1461
abdomen2.47e-1461
subdivision of trunk4.68e-12113
duct of male reproductive system4.74e-124
epithelium of foregut-midgut junction3.46e-1125
anatomical boundary3.46e-1125
hepatobiliary system3.46e-1125
foregut-midgut junction3.46e-1125
septum transversum3.46e-1125
internal genitalia5.43e-1125
renal system1.46e-1045
cavitated compound organ1.79e-1032
kidney4.23e-1027
kidney mesenchyme4.23e-1027
kidney rudiment4.23e-1027
kidney field4.23e-1027
hepatic diverticulum5.17e-1022
liver primordium5.17e-1022
reproductive organ8.67e-1048
digestive tract diverticulum1.55e-0923
reproductive structure3.99e-0959
reproductive system3.99e-0959
adult organism4.33e-09115
urinary system structure6.06e-0944
liver9.86e-0919
digestive gland9.86e-0919
liver bud9.86e-0919
epithelial sac1.08e-0825
mixed endoderm/mesoderm-derived structure1.15e-08130
sac2.54e-0826
endo-epithelium3.01e-0882
duct3.44e-0826
trunk5.60e-08216
anatomical space7.38e-08104
subdivision of digestive tract1.22e-07129
endodermal part of digestive tract1.22e-07129
mesenchyme1.55e-07238
entire embryonic mesenchyme1.55e-07238
male reproductive organ2.74e-0711
renal cortex tubule4.08e-073
region of nephron tubule4.08e-073
proximal tubule4.08e-073
gut epithelium4.89e-0754
intermediate mesoderm6.22e-0737
body cavity precursor6.73e-0763


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.