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|full_id=C3198_salivary_breast_submaxillary_Intestinal_Hepatocyte_Prostate_thyroid
|full_id=C3198_salivary_breast_submaxillary_Intestinal_Hepatocyte_Prostate_thyroid
|id=C3198
|id=C3198
|ontology_enrichment_celltype=CL:0000223!1.85e-15!59;CL:0002076!6.33e-13!43;CL:0000066!4.24e-12!254
|ontology_enrichment_disease=DOID:305!5.73e-08!106;DOID:299!1.18e-07!25;DOID:0050687!5.30e-07!143
|ontology_enrichment_uberon=UBERON:0004119!1.45e-25!169;UBERON:0000925!1.45e-25!169;UBERON:0006595!1.45e-25!169;UBERON:0001007!4.45e-21!155;UBERON:0001555!4.45e-21!155;UBERON:0007026!4.45e-21!155;UBERON:0000481!2.78e-20!347;UBERON:0000466!2.12e-19!126;UBERON:0000475!2.47e-18!365;UBERON:0002100!1.43e-17!216;UBERON:0004921!1.45e-16!129;UBERON:0004185!1.45e-16!129;UBERON:0005177!1.36e-15!107;UBERON:0003104!5.10e-15!238;UBERON:0009142!5.10e-15!238;UBERON:0009569!8.07e-15!113;UBERON:0000077!8.82e-15!130;UBERON:0000464!2.83e-14!104;UBERON:0005911!1.59e-12!82;UBERON:0000062!7.86e-11!511;UBERON:0000468!2.11e-10!659;UBERON:0001008!1.19e-09!45;UBERON:0006554!2.49e-09!44;UBERON:0001041!3.90e-09!98;UBERON:0005256!5.16e-09!143;UBERON:0002553!8.43e-09!70;UBERON:0004111!1.64e-08!241;UBERON:0005172!1.67e-08!55;UBERON:0005173!1.67e-08!55;UBERON:0000922!2.65e-08!612;UBERON:0000160!2.83e-08!27;UBERON:0003929!3.13e-08!54;UBERON:0000161!3.58e-08!35;UBERON:0000915!4.33e-08!52;UBERON:0005409!5.74e-08!35;UBERON:0002417!1.32e-07!61;UBERON:0000916!1.32e-07!61;UBERON:0000477!2.60e-07!286;UBERON:0009497!2.76e-07!25;UBERON:0000015!2.76e-07!25;UBERON:0002423!2.76e-07!25;UBERON:0006235!2.76e-07!25;UBERON:0004161!2.76e-07!25;UBERON:0001048!4.53e-07!168;UBERON:0002365!4.92e-07!31;UBERON:0002330!4.92e-07!31;UBERON:0003886!5.20e-07!63;UBERON:0000165!6.38e-07!28;UBERON:0000930!6.38e-07!28;UBERON:0000483!9.43e-07!309;UBERON:0000058!9.84e-07!26;UBERON:0003064!9.86e-07!37
}}
}}

Revision as of 14:33, 21 May 2012


Full id: C3198_salivary_breast_submaxillary_Intestinal_Hepatocyte_Prostate_thyroid



Phase1 CAGE Peaks

Hg19::chr11:70963538..70963630,-p1@SHANK2
Hg19::chr11:70963809..70963836,-p2@SHANK2
Hg19::chr11:70963843..70963872,-p6@SHANK2


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
endodermal cell1.85e-1559
endo-epithelial cell6.33e-1343
epithelial cell4.24e-12254
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.45e-25169
endoderm1.45e-25169
presumptive endoderm1.45e-25169
digestive system4.45e-21155
digestive tract4.45e-21155
primitive gut4.45e-21155
multi-tissue structure2.78e-20347
immaterial anatomical entity2.12e-19126
organism subdivision2.47e-18365
trunk1.43e-17216
subdivision of digestive tract1.45e-16129
endodermal part of digestive tract1.45e-16129
trunk region element1.36e-15107
mesenchyme5.10e-15238
entire embryonic mesenchyme5.10e-15238
subdivision of trunk8.07e-15113
mixed endoderm/mesoderm-derived structure8.82e-15130
anatomical space2.83e-14104
endo-epithelium1.59e-1282
organ7.86e-11511
multi-cellular organism2.11e-10659
renal system1.19e-0945
urinary system structure2.49e-0944
foregut3.90e-0998
trunk mesenchyme5.16e-09143
anatomical cavity8.43e-0970
anatomical conduit1.64e-08241
abdomen element1.67e-0855
abdominal segment element1.67e-0855
embryo2.65e-08612
intestine2.83e-0827
gut epithelium3.13e-0854
orifice3.58e-0835
thoracic segment of trunk4.33e-0852
gastrointestinal system5.74e-0835
abdominal segment of trunk1.32e-0761
abdomen1.32e-0761
anatomical cluster2.60e-07286
epithelium of foregut-midgut junction2.76e-0725
anatomical boundary2.76e-0725
hepatobiliary system2.76e-0725
foregut-midgut junction2.76e-0725
septum transversum2.76e-0725
primordium4.53e-07168
exocrine gland4.92e-0731
exocrine system4.92e-0731
body cavity precursor5.20e-0763
mouth6.38e-0728
stomodeum6.38e-0728
epithelium9.43e-07309
duct9.84e-0726
intermediate mesoderm9.86e-0737
Disease
Ontology termp-valuen
carcinoma5.73e-08106
adenocarcinoma1.18e-0725
cell type cancer5.30e-07143


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.