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Coexpression cluster:C3008: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000464!8.12e-15!95;UBERON:0001004!2.80e-14!74;UBERON:0004119!7.86e-14!160;UBERON:0000925!7.86e-14!160;UBERON:0006595!7.86e-14!160;UBERON:0000153!3.18e-11!62;UBERON:0007811!3.18e-11!62;UBERON:0000466!2.68e-10!117;UBERON:0000161!2.75e-10!36;UBERON:0000166!2.98e-10!22;UBERON:0005631!3.51e-10!14;UBERON:0000158!3.51e-10!14;UBERON:0000033!8.55e-10!56;UBERON:0001007!1.05e-08!145;UBERON:0001555!1.05e-08!145;UBERON:0007026!1.05e-08!145;UBERON:0003133!1.15e-08!48;UBERON:0000065!1.21e-08!54;UBERON:0001444!1.28e-08!49;UBERON:0003100!2.35e-08!41;UBERON:0001008!2.36e-08!48;UBERON:0005156!2.43e-08!59;UBERON:0000990!2.43e-08!59;UBERON:0005178!3.94e-08!34;UBERON:0002224!3.94e-08!34;UBERON:0002553!5.55e-08!61;UBERON:0003124!6.02e-08!7;UBERON:0006554!6.10e-08!47;UBERON:0001044!8.14e-08!6;UBERON:0003293!8.14e-08!6;UBERON:0003294!8.14e-08!6;UBERON:0010047!8.14e-08!6;UBERON:0000167!8.14e-08!6;UBERON:0005181!1.00e-07!35;UBERON:0000165!1.06e-07!29;UBERON:0000930!1.06e-07!29;UBERON:0005153!1.32e-07!37;UBERON:0001048!4.56e-07!160;UBERON:0005911!6.14e-07!82;UBERON:0000475!7.27e-07!264;UBERON:0003408!7.53e-07!10
|ontology_enrichment_uberon=UBERON:0000464!8.12e-15!95;UBERON:0001004!2.80e-14!74;UBERON:0004119!7.86e-14!160;UBERON:0000925!7.86e-14!160;UBERON:0006595!7.86e-14!160;UBERON:0000153!3.18e-11!62;UBERON:0007811!3.18e-11!62;UBERON:0000466!2.68e-10!117;UBERON:0000161!2.75e-10!36;UBERON:0000166!2.98e-10!22;UBERON:0005631!3.51e-10!14;UBERON:0000158!3.51e-10!14;UBERON:0000033!8.55e-10!56;UBERON:0001007!1.05e-08!145;UBERON:0001555!1.05e-08!145;UBERON:0007026!1.05e-08!145;UBERON:0003133!1.15e-08!48;UBERON:0000065!1.21e-08!54;UBERON:0001444!1.28e-08!49;UBERON:0003100!2.35e-08!41;UBERON:0001008!2.36e-08!48;UBERON:0005156!2.43e-08!59;UBERON:0000990!2.43e-08!59;UBERON:0005178!3.94e-08!34;UBERON:0002224!3.94e-08!34;UBERON:0002553!5.55e-08!61;UBERON:0003124!6.02e-08!7;UBERON:0006554!6.10e-08!47;UBERON:0001044!8.14e-08!6;UBERON:0003293!8.14e-08!6;UBERON:0003294!8.14e-08!6;UBERON:0010047!8.14e-08!6;UBERON:0000167!8.14e-08!6;UBERON:0005181!1.00e-07!35;UBERON:0000165!1.06e-07!29;UBERON:0000930!1.06e-07!29;UBERON:0005153!1.32e-07!37;UBERON:0001048!4.56e-07!160;UBERON:0005911!6.14e-07!82;UBERON:0000475!7.27e-07!264;UBERON:0003408!7.53e-07!10
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}}
}}

Revision as of 15:52, 26 November 2012


Full id: C3008_choriocarcinoma_Small_testicular_Amniotic_oral_pancreatic_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr10:24544249..24544276,+p3@KIAA1217
Hg19::chr10:24544284..24544304,+p6@KIAA1217
Hg19::chr10:24544308..24544313,+p18@KIAA1217


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>

Uber Anatomy
Ontology termp-valuen
anatomical space8.12e-1595
respiratory system2.80e-1474
endoderm-derived structure7.86e-14160
endoderm7.86e-14160
presumptive endoderm7.86e-14160
anterior region of body3.18e-1162
craniocervical region3.18e-1162
immaterial anatomical entity2.68e-10117
orifice2.75e-1036
oral opening2.98e-1022
extraembryonic membrane3.51e-1014
membranous layer3.51e-1014
head8.55e-1056
digestive system1.05e-08145
digestive tract1.05e-08145
primitive gut1.05e-08145
reproductive organ1.15e-0848
respiratory tract1.21e-0854
subdivision of head1.28e-0849
female organism2.35e-0841
renal system2.36e-0848
reproductive structure2.43e-0859
reproductive system2.43e-0859
thoracic cavity element3.94e-0834
thoracic cavity3.94e-0834
anatomical cavity5.55e-0861
chorion6.02e-087
urinary system structure6.10e-0847
saliva-secreting gland8.14e-086
gland of oral region8.14e-086
gland of foregut8.14e-086
oral gland8.14e-086
oral cavity8.14e-086
thoracic segment organ1.00e-0735
mouth1.06e-0729
stomodeum1.06e-0729
epithelial bud1.32e-0737
primordium4.56e-07160
endo-epithelium6.14e-0782
organism subdivision7.27e-07264
gland of gut7.53e-0710
Disease
Ontology termp-valuen
squamous cell carcinoma1.03e-1014


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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