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Coexpression cluster:C3695: Difference between revisions

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|full_id=C3695_large_glioblastoma_Hep2_mesothelioma_cervical_epitheloid_mucinous
|full_id=C3695_large_glioblastoma_Hep2_mesothelioma_cervical_epitheloid_mucinous
|id=C3695
|id=C3695
|ontology_enrichment_celltype=CL:0002150!1.42e-16!3;CL:0000861!1.42e-16!3;CL:0000066!1.17e-10!254
|ontology_enrichment_celltype=CL:0000319!2.74e-10!1;CL:0000066!5.50e-10!253
|ontology_enrichment_disease=DOID:305!3.34e-29!106;DOID:0050687!1.12e-27!143;DOID:162!3.33e-18!235;DOID:14566!1.11e-17!239;DOID:5093!1.10e-11!4;DOID:1612!1.10e-11!4
|ontology_enrichment_disease=DOID:305!5.84e-25!106;DOID:0050687!9.12e-18!143;DOID:162!5.96e-14!235;DOID:14566!1.35e-13!239;DOID:3030!2.74e-10!1
|ontology_enrichment_uberon=UBERON:0001737!2.93e-46!9;UBERON:0001557!6.20e-31!19;UBERON:0000072!5.24e-25!46;UBERON:0008947!9.11e-24!38;UBERON:0003258!9.11e-24!38;UBERON:0000065!3.15e-21!53;UBERON:0001004!1.10e-14!72;UBERON:0001041!2.00e-14!98;UBERON:0000077!1.88e-12!130;UBERON:0004921!4.30e-11!129;UBERON:0004185!4.30e-11!129;UBERON:0001007!9.89e-11!155;UBERON:0001555!9.89e-11!155;UBERON:0007026!9.89e-11!155;UBERON:0000063!5.27e-10!97;UBERON:0004119!1.87e-09!169;UBERON:0000925!1.87e-09!169;UBERON:0006595!1.87e-09!169;UBERON:0001048!1.31e-07!168
|ontology_enrichment_uberon=UBERON:0001737!2.40e-80!9;UBERON:0008947!4.03e-38!38;UBERON:0003258!4.03e-38!38;UBERON:0001557!1.67e-37!19;UBERON:0000072!1.96e-30!47;UBERON:0000065!3.18e-26!54;UBERON:0001004!1.42e-18!74;UBERON:0001041!1.76e-15!87;UBERON:0000063!1.67e-13!98;UBERON:0004921!9.65e-11!118;UBERON:0001007!2.35e-08!145;UBERON:0001555!2.35e-08!145;UBERON:0007026!2.35e-08!145;UBERON:0001048!1.96e-07!160;UBERON:0004119!2.24e-07!160;UBERON:0000925!2.24e-07!160;UBERON:0006595!2.24e-07!160
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325041142014395!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433565762731318!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719892134786364!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301671946063862!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248124722015163!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615511870486921
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325041142014395!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433565762731318!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719892134786364!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301671946063862!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248124722015163!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00615511870486921
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}}
}}

Revision as of 15:19, 19 October 2012


Full id: C3695_large_glioblastoma_Hep2_mesothelioma_cervical_epitheloid_mucinous



Phase1 CAGE Peaks

Hg19::chr17:77743928..77743937,-p@chr17:77743928..77743937
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Hg19::chr17:77743943..77743968,-p@chr17:77743943..77743968
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Hg19::chr17:77743980..77744002,-p@chr17:77743980..77744002
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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
mucus secreting cell2.74e-101
epithelial cell5.50e-10253
Uber Anatomy
Ontology termp-valuen
larynx2.40e-809
respiratory primordium4.03e-3838
endoderm of foregut4.03e-3838
upper respiratory tract1.67e-3719
segment of respiratory tract1.96e-3047
respiratory tract3.18e-2654
respiratory system1.42e-1874
foregut1.76e-1587
organ segment1.67e-1398
subdivision of digestive tract9.65e-11118
digestive system2.35e-08145
digestive tract2.35e-08145
primitive gut2.35e-08145
primordium1.96e-07160
endoderm-derived structure2.24e-07160
endoderm2.24e-07160
presumptive endoderm2.24e-07160
Disease
Ontology termp-valuen
carcinoma5.84e-25106
cell type cancer9.12e-18143
cancer5.96e-14235
disease of cellular proliferation1.35e-13239
mucinous adenocarcinoma2.74e-101


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
E2F1#186934.907389214879320.008460985347239390.0325041142014395
GTF2F1#2962312.73966087675770.0004835525047438590.00433565762731318
MXI1#460139.96157162875930.001011470541259020.00719892134786364
SMARCC1#6599343.66335931963151.20046018043203e-050.000301671946063862
TFAP2A#7020316.5186343730450.0002218033880766340.00248124722015163
TFAP2C#7022310.80922860986020.0007916746575753130.00615511870486921



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.