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Coexpression cluster:C825: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004913!2.55e-98!1;UBERON:0003703!2.55e-98!1;UBERON:0001174!2.55e-98!1;UBERON:0004914!2.55e-98!1;UBERON:0002394!2.83e-66!6;UBERON:0003928!2.83e-66!6;UBERON:0002294!9.75e-45!9;UBERON:0001173!9.75e-45!9;UBERON:0004912!9.75e-45!9;UBERON:0002114!5.96e-34!2;UBERON:0000058!5.37e-22!19;UBERON:0002108!5.15e-21!4;UBERON:0008835!3.41e-19!22;UBERON:0003894!3.41e-19!22;UBERON:0009854!2.02e-18!23;UBERON:0007499!4.64e-17!25;UBERON:0009497!4.64e-17!25;UBERON:0000015!4.64e-17!25;UBERON:0002423!4.64e-17!25;UBERON:0006235!4.64e-17!25;UBERON:0004161!4.64e-17!25;UBERON:0009856!1.86e-16!26;UBERON:0003929!1.34e-08!54;UBERON:0000160!7.60e-07!17
|ontology_enrichment_uberon=UBERON:0004913!2.55e-98!1;UBERON:0003703!2.55e-98!1;UBERON:0001174!2.55e-98!1;UBERON:0004914!2.55e-98!1;UBERON:0002394!2.83e-66!6;UBERON:0003928!2.83e-66!6;UBERON:0002294!9.75e-45!9;UBERON:0001173!9.75e-45!9;UBERON:0004912!9.75e-45!9;UBERON:0002114!5.96e-34!2;UBERON:0000058!5.37e-22!19;UBERON:0002108!5.15e-21!4;UBERON:0008835!3.41e-19!22;UBERON:0003894!3.41e-19!22;UBERON:0009854!2.02e-18!23;UBERON:0007499!4.64e-17!25;UBERON:0009497!4.64e-17!25;UBERON:0000015!4.64e-17!25;UBERON:0002423!4.64e-17!25;UBERON:0006235!4.64e-17!25;UBERON:0004161!4.64e-17!25;UBERON:0009856!1.86e-16!26;UBERON:0003929!1.34e-08!54;UBERON:0000160!7.60e-07!17
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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.101185,0.273994,0.404877,0.237701,0.403356,0.474413,0.140612,0.138703,0.230076,0.375531,1.28238,0.107365,0.46359,0.666154,0.712999,0.68716,0.559826,0.116269,0.0470551,1.3792,0.270268,0.396189,1.90679,0.844704,0.537051,0.641011,0.39419,0.240354,0.0826403,0.355553,0.722879,0.958783,0.715457,0.20845,0.0928746,0.593726,0.404426,0.547451,0.125439,0.597291,0.340749,0.302519,0.235234,0.0391382,0.301189,0.47544,0.365597,1.19951,1.2542,0.550604,0.486559,0.468946,0.797754,0.947672,0.466348,0.244111,0.435652,0.59006,1.10913,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.0579262,0.945703,0.104203,0.0955465,0.610619,0.644006,0.709631,0.309107,0.380738,0.659298,1.23725,0.864635,0.89511,0.0510741,0.0463436,0.0795497,0.575506,1.4989,1.12715,0.868602,0.739223,0.982336,0.238337,0.18161,0.743843,0.780743,0.579925,0.0696508,0.550108,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.590599,0.0136871,0.354459,0.624851,0.173291,0.937551,0.57318,1.03543,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.537508,0.869279,0.358161,0.993705,0.50181,1.13991,0.260985,2.49548,0.394712,1.09788,1.95265,1.55112,1.06096,1.18535,0.777301,0.617705,1.09407,1.46467,1.79367,0.337738,0.503344,0.052013,0.119096,0.869654,0.414185,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.158769,1.192,0.00718895
}}
}}

Revision as of 14:29, 26 November 2012


Full id: C825_bile_papillotubular_mucinous_Neutrophils_Gingival_squamous_giant



Phase1 CAGE Peaks

Hg19::chr13:38307395..38307406,-p@chr13:38307395..38307406
-
Hg19::chr13:38307430..38307446,-p@chr13:38307430..38307446
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Hg19::chr13:38307471..38307497,-p@chr13:38307471..38307497
-
Hg19::chr14:51145019..51145024,+p@chr14:51145019..51145024
+
Hg19::chr14:51145106..51145119,+p@chr14:51145106..51145119
+
Hg19::chr20:56265718..56265764,-p12@PMEPA1
Hg19::chr2:241679478..241679495,+p@chr2:241679478..241679495
+
Hg19::chr6:136947581..136947582,-p@chr6:136947581..136947582
-
Hg19::chr6:136947642..136947673,-p@chr6:136947642..136947673
-
Hg19::chr7:44426058..44426097,-p11@NUDCD3


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
hepatopancreatic ampulla2.55e-981
extrahepatic bile duct2.55e-981
common bile duct2.55e-981
duodenal papilla2.55e-981
bile duct2.83e-666
digestive system duct2.83e-666
biliary system9.75e-459
biliary tree9.75e-459
biliary bud9.75e-459
duodenum5.96e-342
duct5.37e-2219
small intestine5.15e-214
hepatic diverticulum3.41e-1922
liver primordium3.41e-1922
digestive tract diverticulum2.02e-1823
epithelial sac4.64e-1725
epithelium of foregut-midgut junction4.64e-1725
anatomical boundary4.64e-1725
hepatobiliary system4.64e-1725
foregut-midgut junction4.64e-1725
septum transversum4.64e-1725
sac1.86e-1626
gut epithelium1.34e-0854
intestine7.60e-0717
Disease
Ontology termp-valuen
tubular adenocarcinoma4.52e-502
gastrointestinal system cancer2.00e-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)

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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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