Personal tools

Coexpression cluster:C318

From FANTOM5_SSTAR

Revision as of 16:04, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C318_hepatoma_Intestinal_bile_small_colon_Prostate_endometrial



Phase1 CAGE Peaks

Hg19::chr10:5048261..5048285,-p@chr10:5048261..5048285
-
Hg19::chr10:5135981..5136010,+p6@AKR1C3
Hg19::chr11:111154870..111154887,+p2@C11orf53
Hg19::chr11:111154907..111154928,+p1@C11orf53
Hg19::chr11:111154934..111154946,+p3@C11orf53
Hg19::chr11:111154964..111154975,+p4@C11orf53
Hg19::chr11:111175739..111175773,-p6@C11orf92
Hg19::chr11:111175775..111175789,-p7@C11orf92
Hg19::chr11:111176063..111176079,-p8@C11orf92
Hg19::chr11:111176084..111176102,-p9@C11orf92
Hg19::chr11:111176104..111176114,-p11@C11orf92
Hg19::chr11:69715346..69715355,-p@chr11:69715346..69715355
-
Hg19::chr11:69715376..69715382,-p@chr11:69715376..69715382
-
Hg19::chr11:69715408..69715418,-p@chr11:69715408..69715418
-
Hg19::chr14:23445970..23445991,-p6@AJUBA
Hg19::chr14:96734892..96734925,-p1@ENST00000553638
Hg19::chr16:57640858..57640869,-p@chr16:57640858..57640869
-
Hg19::chr19:41509967..41509988,+p3@CYP2B6
Hg19::chr19:41510133..41510160,+p@chr19:41510133..41510160
+
Hg19::chr1:197928283..197928310,+p@chr1:197928283..197928310
+
Hg19::chr3:30226342..30226387,-p@chr3:30226342..30226387
-
Hg19::chr4:72468240..72468271,+p@chr4:72468240..72468271
+
Hg19::chr5:1201465..1201468,+p11@SLC6A19
Hg19::chr5:1201536..1201542,+p4@SLC6A19
Hg19::chr5:1202241..1202252,-p@chr5:1202241..1202252
-
Hg19::chr5:68339691..68339711,-p1@ENST00000479830
Hg19::chr6:132935900..132935911,-p@chr6:132935900..132935911
-
Hg19::chr7:107875370..107875381,-p@chr7:107875370..107875381
-
Hg19::chr8:100519343..100519351,+p@chr8:100519343..100519351
+
Hg19::chr8:100519383..100519390,+p@chr8:100519383..100519390
+
Hg19::chr8:17767866..17767892,-p4@FGL1
Hg19::chr9:22113541..22113546,+p3@CDKN2B-AS
Hg19::chr9:22113608..22113615,+p17@CDKN2B-AS
Hg19::chr9:38437671..38437689,+p@chr9:38437671..38437689
+
Hg19::chr9:38437690..38437712,+p@chr9:38437690..38437712
+
Hg19::chr9:38437716..38437729,+p@chr9:38437716..38437729
+
Hg19::chr9:38437744..38437747,+p@chr9:38437744..38437747
+


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
6.26588234213711e-050.0287703396869713259Arachidonic acid metabolism (KEGG):00590
9.0901547194222e-050.0287703396869713271Metabolism of xenobiotics by cytochrome P450 (KEGG):00980



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:0047017prostaglandin-F synthase activity0.00874172177855952
GO:00470263-alpha-hydroxysteroid dehydrogenase (A-specific) activity0.00874172177855952
GO:0047045testosterone 17-beta-dehydrogenase (NADP+) activity0.00874172177855952
GO:0047115trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity0.00874172177855952
GO:0050327testosterone 17-beta-dehydrogenase activity0.0093240915001036
GO:0005577fibrinogen complex0.0165019362595048
GO:0004033aldo-keto reductase activity0.0165019362595048
GO:0015804neutral amino acid transport0.0165019362595048
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.0165019362595048
GO:0006693prostaglandin metabolic process0.0165019362595048
GO:0006692prostanoid metabolic process0.0165019362595048
GO:0015175neutral amino acid transmembrane transporter activity0.0165019362595048
GO:0006118electron transport0.0201970832734816
GO:0050381unspecific monooxygenase activity0.0216241942435844
GO:0016229steroid dehydrogenase activity0.024833518960349
GO:0006091generation of precursor metabolites and energy0.0272454932255383
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0306091097628793
GO:0006690icosanoid metabolic process0.0306091097628793
GO:0005328neurotransmitter:sodium symporter activity0.0306091097628793
GO:0005326neurotransmitter transporter activity0.0308192896656132
GO:0015171amino acid transmembrane transporter activity0.034874355006795
GO:0006865amino acid transport0.0369765176591999
GO:0006836neurotransmitter transport0.037764746818911
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.037764746818911
GO:0015837amine transport0.037764746818911
GO:0015370solute:sodium symporter activity0.037764746818911
GO:0046943carboxylic acid transmembrane transporter activity0.037764746818911
GO:0046942carboxylic acid transport0.037764746818911
GO:0015849organic acid transport0.037764746818911
GO:0005342organic acid transmembrane transporter activity0.037764746818911
GO:0016491oxidoreductase activity0.037764746818911
GO:0015294solute:cation symporter activity0.0413201004265023



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
epithelial cell1.10e-10254
endodermal cell1.62e-0759
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.54e-20169
endoderm2.54e-20169
presumptive endoderm2.54e-20169
digestive system9.07e-20155
digestive tract9.07e-20155
primitive gut9.07e-20155
subdivision of digestive tract2.84e-18129
endodermal part of digestive tract2.84e-18129
mixed endoderm/mesoderm-derived structure5.51e-16130
multi-tissue structure6.50e-13347
foregut4.42e-1298
organism subdivision1.25e-10365
endo-epithelium1.56e-1082
adult organism4.05e-10115
gut epithelium2.52e-0954
immaterial anatomical entity3.89e-09126
mesenchyme6.97e-09238
entire embryonic mesenchyme6.97e-09238
gastrointestinal system2.76e-0835
trunk region element5.37e-08107
organ5.49e-08511
epithelium of foregut-midgut junction9.96e-0825
anatomical boundary9.96e-0825
hepatobiliary system9.96e-0825
foregut-midgut junction9.96e-0825
septum transversum9.96e-0825
subdivision of trunk1.15e-07113
sac2.17e-0726
primordium4.77e-07168
epithelial sac6.25e-0725
anatomical cluster7.38e-07286
digestive tract diverticulum9.51e-0723
Disease
Ontology termp-valuen
carcinoma2.29e-22106
cell type cancer2.79e-19143
cancer2.09e-10235
disease of cellular proliferation2.17e-09239


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
FOXA2#317063.994129257188960.003515705436370290.0178509776882238
MAFF#2376446.088146647561640.004109374781056080.0195864819623364
MAFK#797553.662261234841880.01113490178151240.040943492136724



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C318&oldid=2137951"