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Coexpression cluster:C3871: Difference between revisions

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|full_id=C3871_nasal_CD14_Alveolar_squamous_Prostate_Tracheal_large
|full_id=C3871_nasal_CD14_Alveolar_squamous_Prostate_Tracheal_large
|id=C3871
|id=C3871
|ontology_enrichment_celltype=CL:0000548!1.97e-27!679;CL:0000004!1.97e-27!679;CL:0000255!1.97e-27!679;CL:0000012!1.83e-26!682;CL:0000066!1.37e-24!254;CL:0000063!3.28e-17!578;CL:0000003!4.13e-15!722;CL:0002371!4.32e-15!591;CL:0000144!5.31e-15!625;CL:0002076!1.03e-13!43;CL:0000220!1.84e-13!246;CL:0002321!6.92e-13!248;CL:0000860!7.17e-11!45;CL:0002057!1.18e-10!42;CL:0000223!6.03e-10!59;CL:0002368!6.80e-09!13;CL:0000076!6.01e-08!62;CL:0002202!8.49e-07!9;CL:0002632!8.49e-07!9
|ontology_enrichment_celltype=CL:0000066!4.28e-23!253;CL:0000548!9.59e-23!679;CL:0000255!9.59e-23!679;CL:0000003!6.52e-14!722;CL:0002076!7.16e-14!42;CL:0002371!6.00e-13!588;CL:0000860!2.89e-12!42;CL:0002057!2.89e-12!42;CL:0002321!1.75e-10!250;CL:0000223!5.98e-10!58;CL:0002368!1.13e-09!13;CL:0000473!6.22e-09!48;CL:0000234!6.22e-09!48;CL:0002202!2.91e-07!9;CL:0002632!2.91e-07!9;CL:0000076!6.56e-07!63
|ontology_enrichment_disease=DOID:1749!1.87e-07!14
|ontology_enrichment_disease=DOID:1749!6.70e-08!14
|ontology_enrichment_uberon=UBERON:0000926!5.93e-12!448;UBERON:0004120!5.93e-12!448;UBERON:0006603!5.93e-12!448;UBERON:0000467!1.72e-10!625;UBERON:0000480!2.76e-10!626;UBERON:0003102!9.49e-10!95;UBERON:0002050!1.36e-09!605;UBERON:0005423!1.36e-09!605;UBERON:0000923!1.38e-09!604;UBERON:0005291!1.38e-09!604;UBERON:0006598!1.38e-09!604;UBERON:0002532!1.38e-09!604;UBERON:0000468!7.89e-09!659;UBERON:0000922!8.56e-09!612;UBERON:0000062!1.15e-08!511;UBERON:0003104!3.22e-07!238;UBERON:0009142!3.22e-07!238;UBERON:0004119!3.61e-07!169;UBERON:0000925!3.61e-07!169;UBERON:0006595!3.61e-07!169;UBERON:0001444!5.67e-07!48;UBERON:0002204!5.71e-07!167
|ontology_enrichment_uberon=UBERON:0000467!8.19e-09!624;UBERON:0000480!1.14e-08!625;UBERON:0003102!1.43e-08!99;UBERON:0000033!1.11e-07!56;UBERON:0001444!3.49e-07!49;UBERON:0000475!5.37e-07!264;UBERON:0000468!8.23e-07!656
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915487780230736!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897685693336501!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00581429809355155!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433975595453673!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444265241382293!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015681118932076!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186576249849695!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294584348160277!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309075846224874!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172967971358867!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203045621187879!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301744550623684
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915487780230736!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00897685693336501!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00581429809355155!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433975595453673!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444265241382293!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015681118932076!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186576249849695!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294584348160277!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309075846224874!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172967971358867!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203045621187879!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301744550623684
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}}
}}

Revision as of 15:28, 19 October 2012


Full id: C3871_nasal_CD14_Alveolar_squamous_Prostate_Tracheal_large



Phase1 CAGE Peaks

Hg19::chr1:153538246..153538265,-p7@S100A2
Hg19::chr1:153538268..153538288,-p4@S100A2
Hg19::chr1:153538292..153538342,-p3@S100A2


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 system8.19e-09624
anatomical group1.14e-08625
surface structure1.43e-0899
head1.11e-0756
subdivision of head3.49e-0749
organism subdivision5.37e-07264
multi-cellular organism8.23e-07656
Disease
Ontology termp-valuen
squamous cell carcinoma6.70e-0814


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
EBF1#187938.9064668465690.00141523283560980.00915487780230736
FOS#235338.99795530889440.001372499272417130.00897685693336501
FOXA1#3169311.08141974938550.000734755275698670.00581429809355155
GTF2F1#2962312.73966087675770.0004835525047438590.00433975595453673
JUN#3725312.51282919233630.0005103313992726250.00444265241382293
JUND#372736.994663941871030.002921845042734990.015681118932076
MAX#414936.452555509007120.003721913834265510.0186576249849695
MYC#460935.22228187160940.007020843755740150.0294584348160277
NR3C1#2908314.9730233311730.0002978331194675480.00309075846224874
PAX5#507936.669565531177830.003370290999677260.0172967971358867
SMARCB1#6598318.25271578115740.000164397760679890.00203045621187879
SMARCC1#6599343.66335931963151.20046018043203e-050.000301744550623684



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.