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Coexpression cluster:C3638: Difference between revisions

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|full_id=C3638_serous_seminal_ductus_clear_endometrial_endometrioid_epididymis
|full_id=C3638_serous_seminal_ductus_clear_endometrial_endometrioid_epididymis
|id=C3638
|id=C3638
|ontology_enrichment_celltype=CL:1000507!9.54e-18!12;CL:1000494!9.54e-18!12;CL:1000497!3.66e-16!18;CL:0002518!3.66e-16!18;CL:1000449!1.73e-15!16;CL:0002149!1.24e-10!6;CL:0002255!1.24e-10!6;CL:0002681!2.56e-10!13;CL:0002584!2.56e-10!13;CL:0000239!5.45e-08!3;CL:1000615!5.45e-08!3;CL:0002306!5.45e-08!3;CL:0000066!8.05e-08!254;CL:0000064!1.62e-07!3;CL:0005012!1.62e-07!3;CL:0000067!1.62e-07!3;CL:0002304!1.62e-07!3
|ontology_enrichment_celltype=CL:0000313!4.73e-15!1;CL:0000159!3.56e-08!2
|ontology_enrichment_disease=DOID:299!2.25e-13!25;DOID:3001!1.24e-10!6
|ontology_enrichment_disease=DOID:2152!4.73e-15!1;DOID:4468!4.69e-08!2
|ontology_enrichment_uberon=UBERON:0003887!2.32e-24!21;UBERON:0001008!5.31e-21!45;UBERON:0004876!4.50e-20!20;UBERON:0006554!1.28e-19!44;UBERON:0000080!1.67e-19!18;UBERON:0002120!1.67e-19!18;UBERON:0004875!1.67e-19!18;UBERON:0005721!1.67e-19!18;UBERON:0005754!1.67e-19!18;UBERON:0007297!1.67e-19!18;UBERON:0000058!2.91e-19!26;UBERON:0002113!9.24e-19!27;UBERON:0003918!9.24e-19!27;UBERON:0005095!9.24e-19!27;UBERON:0007687!9.24e-19!27;UBERON:0005172!7.23e-18!55;UBERON:0005173!7.23e-18!55;UBERON:0009773!9.54e-18!12;UBERON:0001231!9.54e-18!12;UBERON:0004810!9.54e-18!12;UBERON:0006555!1.81e-17!17;UBERON:0005103!1.81e-17!17;UBERON:0000083!1.81e-17!17;UBERON:0009201!1.81e-17!17;UBERON:0004819!1.81e-17!17;UBERON:0006553!1.81e-17!17;UBERON:0003074!1.81e-17!17;UBERON:0003060!1.81e-17!17;UBERON:0000489!5.29e-17!32;UBERON:0003064!1.58e-15!37;UBERON:0004211!1.73e-15!16;UBERON:0001285!1.73e-15!16;UBERON:0007684!1.73e-15!16;UBERON:0003220!1.73e-15!16;UBERON:0004208!1.73e-15!16;UBERON:0002417!1.99e-15!61;UBERON:0000916!1.99e-15!61;UBERON:0004175!2.86e-13!25;UBERON:0003886!3.15e-11!63;UBERON:0003133!4.89e-11!48;UBERON:0005156!2.39e-10!59;UBERON:0000990!2.39e-10!59;UBERON:0001225!2.56e-10!13;UBERON:0008987!2.56e-10!13;UBERON:0000488!1.44e-09!4;UBERON:0002553!1.54e-09!70;UBERON:0005177!5.84e-09!107;UBERON:0005795!9.28e-09!22;UBERON:0003975!1.12e-08!22;UBERON:0006947!1.33e-08!3;UBERON:0004054!1.33e-08!3;UBERON:0001851!4.37e-08!16;UBERON:0006853!5.45e-08!3;UBERON:0007685!5.45e-08!3;UBERON:0004134!5.45e-08!3;UBERON:0000466!9.11e-08!126;UBERON:0000353!1.61e-07!17;UBERON:0001778!1.62e-07!3;UBERON:0001775!1.62e-07!3;UBERON:0003134!1.69e-07!37;UBERON:0000474!1.69e-07!37;UBERON:0009569!1.78e-07!113;UBERON:0000995!1.82e-07!21;UBERON:0004177!8.53e-07!7
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}}
}}

Revision as of 15:17, 19 October 2012


Full id: C3638_serous_seminal_ductus_clear_endometrial_endometrioid_epididymis



Phase1 CAGE Peaks

Hg19::chr17:42100581..42100589,-p@chr17:42100581..42100589
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Hg19::chr17:42101153..42101171,-p@chr17:42101153..42101171
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Hg19::chr1:206288186..206288203,-p1@C1orf186


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>disease_data<br>


Cell Type
Ontology termp-valuen
serous secreting cell4.73e-151
seromucus secreting cell3.56e-082
Uber Anatomy
Ontology termp-valuen
male genital duct3.86e-413
internal male genitalia3.86e-413
duct of male reproductive system4.66e-314
male reproductive organ9.44e-2011
internal genitalia6.59e-1925
reproductive structure2.83e-1759
reproductive system2.83e-1759
reproductive organ5.37e-1748
male organism4.13e-1522
male reproductive system4.13e-1522
epithelium of female gonad4.73e-151
seminal vesicle5.42e-151
seminal fluid secreting gland5.42e-151
vas deferens6.22e-151
spermatic cord6.22e-151
epididymis7.13e-151
uterus or analog9.36e-151
urinary system structure6.82e-1047
renal system1.11e-0948
kidney1.54e-0826
kidney mesenchyme1.54e-0826
upper urinary tract1.54e-0826
kidney rudiment1.54e-0826
kidney field1.54e-0826
adult organism1.90e-08114
epithelium of gonad3.56e-082
testis1.45e-078
cavitated compound organ3.42e-0731
duct5.30e-0719
mesonephros5.86e-079
pronephros5.86e-079
nephrogenic cord5.86e-079
pronephric mesoderm5.86e-079
rostral part of nephrogenic cord5.86e-079
presumptive pronephric mesoderm5.86e-079
Disease
Ontology termp-valuen
ovary epithelial cancer4.73e-151
clear cell adenocarcinoma4.69e-082


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.