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Coexpression cluster:C1825: Difference between revisions

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|pathway_enrichment=2.20782089021958e-06;0.00139755062350899;2;25;Maturity onset diabetes of the young (KEGG):04950!4.73033289875392e-05;0.0149715036245562;2;114;Regulation of beta-cell development (Reactome):REACT_13698
|pathway_enrichment=2.20782089021958e-06;0.00139755062350899;2;25;Maturity onset diabetes of the young (KEGG):04950!4.73033289875392e-05;0.0149715036245562;2;114;Regulation of beta-cell development (Reactome):REACT_13698
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}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1825_pancreas_Hepatocyte_liver_colon_gastric_hepatoma_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr19:46367576..46367592,+p1@FOXA3
Hg19::chr1:199996702..199996732,+p5@NR5A2
Hg19::chr1:199996733..199996781,+p1@NR5A2
Hg19::chr6:107235378..107235418,-p1@ENST00000430094
Hg19::chrX:2882296..2882356,-p1@ARSE


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

p.valueFDRnGenesnPathwayName
2.20782089021958e-060.00139755062350899225Maturity onset diabetes of the young (KEGG):04950
4.73033289875392e-050.01497150362455622114Regulation of beta-cell development (Reactome):REACT_13698



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

GO IDGO nameFDR corrected p-value
GO:0003702RNA polymerase II transcription factor activity0.0105280880666253
GO:0001678cell glucose homeostasis0.0105280880666253
GO:0042592homeostatic process0.0105280880666253
GO:0009267cellular response to starvation0.0105280880666253
GO:0031669cellular response to nutrient levels0.0105280880666253
GO:0004065arylsulfatase activity0.0105280880666253
GO:0042594response to starvation0.0105280880666253
GO:0031668cellular response to extracellular stimulus0.0105280880666253
GO:0042593glucose homeostasis0.0105280880666253
GO:0033554cellular response to stress0.0105280880666253
GO:0033500carbohydrate homeostasis0.0105280880666253
GO:0043565sequence-specific DNA binding0.0130242900715327
GO:0051716cellular response to stimulus0.0130242900715327
GO:0065008regulation of biological quality0.0130242900715327
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0130242900715327
GO:0008484sulfuric ester hydrolase activity0.0144693029843891
GO:0003704specific RNA polymerase II transcription factor activity0.016593720844225
GO:0031667response to nutrient levels0.0238504556699512
GO:0003700transcription factor activity0.0238504556699512
GO:0009991response to extracellular stimulus0.0238504556699512
GO:0048856anatomical structure development0.0383789720749396
GO:0003707steroid hormone receptor activity0.0383789720749396
GO:0007275multicellular organismal development0.0459567706342884
GO:0004879ligand-dependent nuclear receptor activity0.0459567706342884



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
metabolising cell3.73e-1712
endopolyploid cell3.73e-1712
parenchymal cell3.73e-1712
polyploid cell3.73e-1712
hepatocyte3.73e-1712
endodermal cell1.99e-0958
Uber Anatomy
Ontology termp-valuen
digestive tract diverticulum4.06e-2923
gastrointestinal system1.35e-2825
epithelium of foregut-midgut junction9.76e-2725
anatomical boundary9.76e-2725
hepatobiliary system9.76e-2725
foregut-midgut junction9.76e-2725
septum transversum9.76e-2725
hepatic diverticulum1.22e-2622
liver primordium1.22e-2622
sac2.58e-2526
intestine2.56e-2417
subdivision of digestive tract2.64e-23118
epithelial sac5.05e-2325
abdomen element9.75e-2054
abdominal segment element9.75e-2054
liver1.16e-1919
digestive gland1.16e-1919
liver bud1.16e-1919
gut epithelium1.88e-1954
digestive system8.74e-19145
digestive tract8.74e-19145
primitive gut8.74e-19145
abdominal segment of trunk3.06e-1760
abdomen3.06e-1760
endoderm-derived structure3.26e-16160
endoderm3.26e-16160
presumptive endoderm3.26e-16160
large intestine4.80e-1411
endo-epithelium7.89e-1482
trunk region element6.65e-13101
exocrine gland4.36e-1131
exocrine system4.36e-1131
small intestine4.76e-114
lower digestive tract9.80e-115
organ system subdivision1.35e-10223
foregut4.92e-1087
endocrine system5.85e-1045
mesenchyme7.20e-10160
entire embryonic mesenchyme7.20e-10160
endocrine gland1.52e-0935
colon3.49e-099
gland3.97e-0959
immaterial anatomical entity4.62e-09117
subdivision of trunk7.93e-09112
rectum4.67e-084
multi-tissue structure5.19e-08342
anatomical cluster1.33e-07373
trunk2.40e-07199
hindgut2.70e-0719
Disease
Ontology termp-valuen
adenocarcinoma8.78e-0925
carcinoma3.43e-08106
gastrointestinal system cancer1.08e-0714
signet ring cell adenocarcinoma1.67e-072
tubular adenocarcinoma1.90e-072


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

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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