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Coexpression cluster:C3123: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004459!L-lactate dehydrogenase activity!0.00333608069390478!3939$GO:0019642!anaerobic glycolysis!0.00333608069390478!3939$GO:0004457!lactate dehydrogenase activity!0.00333608069390478!3939$GO:0006100!tricarboxylic acid cycle intermediate metabolic process!0.00800659366537148!3939$GO:0006096!glycolysis!0.0137255891406368!3939$GO:0006007!glucose catabolic process!0.0137255891406368!3939$GO:0019320!hexose catabolic process!0.0137255891406368!3939$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0137255891406368!3939$GO:0046365!monosaccharide catabolic process!0.0137255891406368!3939$GO:0046164!alcohol catabolic process!0.0137255891406368!3939$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0137255891406368!3939$GO:0044275!cellular carbohydrate catabolic process!0.0137255891406368!3939$GO:0016052!carbohydrate catabolic process!0.0137255891406368!3939$GO:0006006!glucose metabolic process!0.0137255891406368!3939$GO:0019318!hexose metabolic process!0.0171391145649358!3939$GO:0005996!monosaccharide metabolic process!0.0171391145649358!3939$GO:0006066!alcohol metabolic process!0.0261980454491934!3939$GO:0044262!cellular carbohydrate metabolic process!0.0275490032038769!3939$GO:0044265!cellular macromolecule catabolic process!0.0275490032038769!3939$GO:0005829!cytosol!0.0284234075120688!3939$GO:0009057!macromolecule catabolic process!0.029786434767007!3939$GO:0005975!carbohydrate metabolic process!0.03520290367003!3939$GO:0044248!cellular catabolic process!0.03520290367003!3939$GO:0009056!catabolic process!0.0405750814396169!3939
|gostat_on_coexpression_clusters=GO:0004459!L-lactate dehydrogenase activity!0.00333608069390478!3939$GO:0019642!anaerobic glycolysis!0.00333608069390478!3939$GO:0004457!lactate dehydrogenase activity!0.00333608069390478!3939$GO:0006100!tricarboxylic acid cycle intermediate metabolic process!0.00800659366537148!3939$GO:0006096!glycolysis!0.0137255891406368!3939$GO:0006007!glucose catabolic process!0.0137255891406368!3939$GO:0019320!hexose catabolic process!0.0137255891406368!3939$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0137255891406368!3939$GO:0046365!monosaccharide catabolic process!0.0137255891406368!3939$GO:0046164!alcohol catabolic process!0.0137255891406368!3939$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0137255891406368!3939$GO:0044275!cellular carbohydrate catabolic process!0.0137255891406368!3939$GO:0016052!carbohydrate catabolic process!0.0137255891406368!3939$GO:0006006!glucose metabolic process!0.0137255891406368!3939$GO:0019318!hexose metabolic process!0.0171391145649358!3939$GO:0005996!monosaccharide metabolic process!0.0171391145649358!3939$GO:0006066!alcohol metabolic process!0.0261980454491934!3939$GO:0044262!cellular carbohydrate metabolic process!0.0275490032038769!3939$GO:0044265!cellular macromolecule catabolic process!0.0275490032038769!3939$GO:0005829!cytosol!0.0284234075120688!3939$GO:0009057!macromolecule catabolic process!0.029786434767007!3939$GO:0005975!carbohydrate metabolic process!0.03520290367003!3939$GO:0044248!cellular catabolic process!0.03520290367003!3939$GO:0009056!catabolic process!0.0405750814396169!3939
|id=C3123
|id=C3123
|ontology_enrichment_celltype=CL:0000012!1.91e-29!682;CL:0000548!2.73e-29!679;CL:0000004!2.73e-29!679;CL:0000255!2.73e-29!679;CL:0000144!6.61e-22!625;CL:0000055!3.10e-21!180;CL:0002371!2.90e-20!591;CL:0000003!6.14e-18!722;CL:0000063!5.33e-14!578;CL:0000057!8.92e-13!75;CL:0000359!2.98e-09!32;CL:0000034!4.93e-09!444;CL:0000723!6.22e-09!436;CL:0000048!9.48e-09!430;CL:0002620!9.79e-09!23;CL:0000220!1.70e-08!246;CL:0002321!2.44e-08!248;CL:0000680!8.31e-08!57;CL:0000056!8.31e-08!57;CL:0000355!8.31e-08!57;CL:0000192!3.70e-07!42;CL:0000514!3.70e-07!42;CL:0000187!4.57e-07!54
|ontology_enrichment_celltype=CL:0000548!2.14e-28!679;CL:0000255!2.14e-28!679;CL:0002371!3.04e-19!588;CL:0000003!2.57e-17!722;CL:0000057!1.72e-13!76;CL:0000359!1.31e-09!32;CL:0000034!5.90e-09!441;CL:0000723!7.04e-09!433;CL:0002620!7.79e-09!23;CL:0000048!1.05e-08!427;CL:0000055!3.17e-08!106;CL:0002321!6.33e-08!250;CL:0000680!1.66e-07!58;CL:0000056!1.66e-07!58;CL:0000355!1.66e-07!58;CL:0000192!6.34e-07!43;CL:0000514!6.34e-07!43;CL:0000187!8.89e-07!55
|ontology_enrichment_disease=DOID:14566!1.66e-07!239;DOID:162!3.25e-07!235
|ontology_enrichment_disease=DOID:14566!4.44e-07!239;DOID:162!7.08e-07!235
|ontology_enrichment_uberon=UBERON:0001637!6.30e-11!42;UBERON:0003509!6.30e-11!42;UBERON:0004572!6.30e-11!42;UBERON:0000914!1.20e-09!83;UBERON:0002329!1.20e-09!83;UBERON:0003077!1.20e-09!83;UBERON:0003059!1.20e-09!83;UBERON:0007282!1.20e-09!83;UBERON:0009618!1.20e-09!83;UBERON:0007285!1.20e-09!83;UBERON:0000486!1.82e-09!82;UBERON:0002199!2.01e-09!45;UBERON:0002416!2.01e-09!45;UBERON:0004290!4.77e-09!70;UBERON:0004573!9.98e-09!33;UBERON:0004571!9.98e-09!33;UBERON:0002100!2.27e-08!216;UBERON:0002097!2.74e-08!40;UBERON:0000490!8.11e-08!138;UBERON:0004872!1.21e-07!84;UBERON:0005256!1.98e-07!143;UBERON:0003102!2.05e-07!95;UBERON:0001981!2.96e-07!60;UBERON:0007500!2.96e-07!60;UBERON:0004537!2.96e-07!60;UBERON:0006965!2.96e-07!60;UBERON:0001134!3.89e-07!61;UBERON:0002036!3.89e-07!61;UBERON:0003082!3.89e-07!61;UBERON:0002385!6.04e-07!63;UBERON:0001015!6.04e-07!63;UBERON:0000383!6.04e-07!63
|ontology_enrichment_uberon=UBERON:0001637!5.30e-11!42;UBERON:0003509!5.30e-11!42;UBERON:0004572!5.30e-11!42;UBERON:0002199!1.23e-09!46;UBERON:0002416!1.23e-09!46;UBERON:0000486!4.01e-09!83;UBERON:0000490!4.98e-09!148;UBERON:0002329!1.08e-08!71;UBERON:0003059!1.08e-08!71;UBERON:0007282!1.08e-08!71;UBERON:0004290!1.08e-08!71;UBERON:0009618!1.08e-08!71;UBERON:0004573!1.36e-08!33;UBERON:0004571!1.36e-08!33;UBERON:0002097!1.96e-08!41;UBERON:0003102!2.06e-08!99;UBERON:0007524!2.70e-08!73;UBERON:0003077!3.65e-08!72;UBERON:0007285!3.65e-08!72;UBERON:0004872!1.11e-07!83;UBERON:0002100!1.15e-07!199;UBERON:0007500!4.12e-07!59;UBERON:0001981!4.12e-07!59;UBERON:0004537!4.12e-07!59;UBERON:0006965!4.12e-07!59;UBERON:0007503!5.55e-07!78;UBERON:0001134!7.61e-07!62;UBERON:0002036!7.61e-07!62;UBERON:0003082!7.61e-07!62
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296107676831855!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155740273887238!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246686580337135!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179666238384502!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00676762258796965!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191050652838525!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324734092375287!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460105390294214!RDBP#7936;2:102.425602660017:0.000126437939273122:0.00168260090975352!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329709435225185!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287435711201606!TAL1#6886;2:19.9124111182935:0.00328717660874055:0.0170081465365496!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0377970359412001
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296107676831855!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155740273887238!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246686580337135!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179666238384502!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00676762258796965!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191050652838525!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324734092375287!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460105390294214!RDBP#7936;2:102.425602660017:0.000126437939273122:0.00168260090975352!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329709435225185!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287435711201606!TAL1#6886;2:19.9124111182935:0.00328717660874055:0.0170081465365496!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0377970359412001
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}}
}}

Revision as of 14:49, 19 October 2012


Full id: C3123_basal_Adipocyte_Preadipocyte_Olfactory_serous_mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr11:18416103..18416118,+p1@LDHA
Hg19::chr11:18416135..18416147,+p2@LDHA
Hg19::chr9:14922428..14922432,-p1@LDHAP4


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


GO IDGO nameFDR corrected p-value
GO:0004459L-lactate dehydrogenase activity0.00333608069390478
GO:0019642anaerobic glycolysis0.00333608069390478
GO:0004457lactate dehydrogenase activity0.00333608069390478
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.00800659366537148
GO:0006096glycolysis0.0137255891406368
GO:0006007glucose catabolic process0.0137255891406368
GO:0019320hexose catabolic process0.0137255891406368
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0137255891406368
GO:0046365monosaccharide catabolic process0.0137255891406368
GO:0046164alcohol catabolic process0.0137255891406368
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0137255891406368
GO:0044275cellular carbohydrate catabolic process0.0137255891406368
GO:0016052carbohydrate catabolic process0.0137255891406368
GO:0006006glucose metabolic process0.0137255891406368
GO:0019318hexose metabolic process0.0171391145649358
GO:0005996monosaccharide metabolic process0.0171391145649358
GO:0006066alcohol metabolic process0.0261980454491934
GO:0044262cellular carbohydrate metabolic process0.0275490032038769
GO:0044265cellular macromolecule catabolic process0.0275490032038769
GO:0005829cytosol0.0284234075120688
GO:0009057macromolecule catabolic process0.029786434767007
GO:0005975carbohydrate metabolic process0.03520290367003
GO:0044248cellular catabolic process0.03520290367003
GO:0009056catabolic process0.0405750814396169



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
animal cell2.14e-28679
eukaryotic cell2.14e-28679
somatic cell3.04e-19588
native cell2.57e-17722
fibroblast1.72e-1376
vascular associated smooth muscle cell1.31e-0932
stem cell5.90e-09441
somatic stem cell7.04e-09433
skin fibroblast7.79e-0923
multi fate stem cell1.05e-08427
non-terminally differentiated cell3.17e-08106
embryonic cell6.33e-08250
muscle precursor cell1.66e-0758
myoblast1.66e-0758
multi-potent skeletal muscle stem cell1.66e-0758
smooth muscle cell6.34e-0743
smooth muscle myoblast6.34e-0743
muscle cell8.89e-0755
Uber Anatomy
Ontology termp-valuen
artery5.30e-1142
arterial blood vessel5.30e-1142
arterial system5.30e-1142
integument1.23e-0946
integumental system1.23e-0946
multilaminar epithelium4.01e-0983
unilaminar epithelium4.98e-09148
somite1.08e-0871
presomitic mesoderm1.08e-0871
presumptive segmental plate1.08e-0871
dermomyotome1.08e-0871
trunk paraxial mesoderm1.08e-0871
systemic artery1.36e-0833
systemic arterial system1.36e-0833
skin of body1.96e-0841
surface structure2.06e-0899
dense mesenchyme tissue2.70e-0873
paraxial mesoderm3.65e-0872
presumptive paraxial mesoderm3.65e-0872
splanchnic layer of lateral plate mesoderm1.11e-0783
trunk1.15e-07199
epithelial tube open at both ends4.12e-0759
blood vessel4.12e-0759
blood vasculature4.12e-0759
vascular cord4.12e-0759
epithelial vesicle5.55e-0778
skeletal muscle tissue7.61e-0762
striated muscle tissue7.61e-0762
myotome7.61e-0762
Disease
Ontology termp-valuen
disease of cellular proliferation4.44e-07239
cancer7.08e-07235


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
BRCA1#672213.45615376214920.007119807716084560.0296107676831855
GTF2B#2959221.29588662288280.002878180589911410.0155740273887238
HNF4A#3172215.42152690863580.005444210486686610.0246686580337135
HNF4G#3174219.16894835096450.003543986611284220.0179666238384502
MAFF#23764237.54357099329680.0009344774015560320.00676762258796965
MAFK#7975218.06715542521990.003983674744936810.0191050652838525
MEF2A#4205212.4954872730960.008235029478029740.0324734092375287
NR3C1#290829.982015554115360.01278474365547170.0460105390294214
RDBP#79362102.4256026600170.0001264379392731220.00168260090975352
SMARCB1#6598212.16847718743830.008675002221921740.0329709435225185
STAT1#6772213.80439166479950.006770931708444080.0287435711201606
TAL1#6886219.91241111829350.003287176608740550.0170081465365496
ZEB1#6935211.25895467836260.01010222676646330.0377970359412001



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.