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Coexpression cluster:C1523: Difference between revisions

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|full_id=C1523_diffuse_small_lymphoma_thymus_Burkitt_lymphangiectasia_b
|full_id=C1523_diffuse_small_lymphoma_thymus_Burkitt_lymphangiectasia_b
|id=C1523
|id=C1523
|ontology_enrichment_celltype=CL:0002076!2.46e-17!43;CL:0000066!9.85e-17!254;CL:0000223!3.70e-15!59;CL:0000945!1.55e-10!24;CL:0000826!1.55e-10!24;CL:0002251!4.41e-08!21;CL:0000236!1.49e-07!14;CL:0002368!7.73e-07!13
|ontology_enrichment_celltype=CL:0002076!9.40e-12!42;CL:0000066!1.03e-11!253;CL:0000945!3.04e-10!24;CL:0000826!3.04e-10!24;CL:0000223!5.37e-10!58;CL:0002251!3.02e-08!20
|ontology_enrichment_disease=DOID:305!1.85e-12!106;DOID:1749!5.54e-08!14
|ontology_enrichment_disease=DOID:305!1.82e-09!106;DOID:1749!7.67e-09!14
|ontology_enrichment_uberon=UBERON:0004119!1.52e-19!169;UBERON:0000925!1.52e-19!169;UBERON:0006595!1.52e-19!169;UBERON:0001007!1.48e-16!155;UBERON:0001555!1.48e-16!155;UBERON:0007026!1.48e-16!155;UBERON:0004921!2.27e-14!129;UBERON:0004185!2.27e-14!129;UBERON:0001004!1.08e-10!72;UBERON:0000077!1.46e-10!130;UBERON:0005911!1.10e-09!82;UBERON:0000161!1.91e-08!35;UBERON:0005177!2.22e-08!107;UBERON:0001041!3.42e-08!98;UBERON:0001008!5.73e-08!45;UBERON:0000466!6.49e-08!126;UBERON:0000464!1.03e-07!104;UBERON:0006554!1.22e-07!44;UBERON:0000166!5.93e-07!21;UBERON:0005153!7.73e-07!37;UBERON:0000065!7.88e-07!53;UBERON:0005409!9.45e-07!35
|ontology_enrichment_uberon=UBERON:0004119!1.12e-18!160;UBERON:0000925!1.12e-18!160;UBERON:0006595!1.12e-18!160;UBERON:0001007!4.42e-15!145;UBERON:0001555!4.42e-15!145;UBERON:0007026!4.42e-15!145;UBERON:0004921!1.99e-12!118;UBERON:0000153!1.03e-10!62;UBERON:0007811!1.03e-10!62;UBERON:0000161!2.82e-10!36;UBERON:0001004!4.16e-10!74;UBERON:0005911!1.44e-08!82;UBERON:0000033!1.58e-08!56;UBERON:0000166!3.28e-08!22;UBERON:0001444!8.23e-08!49;UBERON:0005409!1.38e-07!25
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755873034325349!E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112781911853599!FOXA1#3169;6:11.0814197493855:5.39600313513231e-07:2.50802479497144e-05!HMGN3#9324;6:8.17854772335059:3.33956428934731e-06:0.000111538456928412!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380676898027587!RXRA#6256;6:20.0746171391333:1.52561140845922e-08:1.11891383348365e-06!SPI1#6688;6:8.20432350852273:3.27709771841866e-06:0.000109592317839874!TRIM28#10155;6:18.5905250452625:2.41896703530258e-08:1.69667225117506e-06
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755873034325349!E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112781911853599!FOXA1#3169;6:11.0814197493855:5.39600313513231e-07:2.50802479497144e-05!HMGN3#9324;6:8.17854772335059:3.33956428934731e-06:0.000111538456928412!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380676898027587!RXRA#6256;6:20.0746171391333:1.52561140845922e-08:1.11891383348365e-06!SPI1#6688;6:8.20432350852273:3.27709771841866e-06:0.000109592317839874!TRIM28#10155;6:18.5905250452625:2.41896703530258e-08:1.69667225117506e-06
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}}
}}

Revision as of 11:23, 19 October 2012


Full id: C1523_diffuse_small_lymphoma_thymus_Burkitt_lymphangiectasia_b



Phase1 CAGE Peaks

Hg19::chr4:74486068..74486079,-p7@RASSF6
Hg19::chr4:74486082..74486085,-p9@RASSF6
Hg19::chr4:74486090..74486106,-p2@RASSF6
Hg19::chr4:74486109..74486166,-p1@RASSF6
Hg19::chr4:74486249..74486273,-p4@RASSF6
Hg19::chr4:74486279..74486297,-p5@RASSF6


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
endo-epithelial cell9.40e-1242
epithelial cell1.03e-11253
lymphocyte of B lineage3.04e-1024
pro-B cell3.04e-1024
endodermal cell5.37e-1058
epithelial cell of alimentary canal3.02e-0820
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.12e-18160
endoderm1.12e-18160
presumptive endoderm1.12e-18160
digestive system4.42e-15145
digestive tract4.42e-15145
primitive gut4.42e-15145
subdivision of digestive tract1.99e-12118
anterior region of body1.03e-1062
craniocervical region1.03e-1062
orifice2.82e-1036
respiratory system4.16e-1074
endo-epithelium1.44e-0882
head1.58e-0856
oral opening3.28e-0822
subdivision of head8.23e-0849
gastrointestinal system1.38e-0725
Disease
Ontology termp-valuen
carcinoma1.82e-09106
squamous cell carcinoma7.67e-0914


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066465.360256373075034.21437267579784e-050.000755873034325349
E2F1#186964.907389214879327.15746523583771e-050.00112781911853599
FOXA1#3169611.08141974938555.39600313513231e-072.50802479497144e-05
HMGN3#932468.178547723350593.33956428934731e-060.000111538456928412
POLR2A#543062.147453176558070.01019570676818780.0380676898027587
RXRA#6256620.07461713913331.52561140845922e-081.11891383348365e-06
SPI1#668868.204323508522733.27709771841866e-060.000109592317839874
TRIM28#10155618.59052504526252.41896703530258e-081.69667225117506e-06



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.