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Coexpression cluster:C4738: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.49e-25!106;DOID:0050687!1.26e-24!143;DOID:162!3.51e-12!235;DOID:14566!5.02e-11!239;DOID:299!9.79e-08!25
|ontology_enrichment_disease=DOID:305!2.49e-25!106;DOID:0050687!1.26e-24!143;DOID:162!3.51e-12!235;DOID:14566!5.02e-11!239;DOID:299!9.79e-08!25
|ontology_enrichment_uberon=UBERON:0007023!1.08e-34!115;UBERON:0001007!3.93e-22!155;UBERON:0001555!3.93e-22!155;UBERON:0007026!3.93e-22!155;UBERON:0004119!7.44e-21!169;UBERON:0000925!7.44e-21!169;UBERON:0006595!7.44e-21!169;UBERON:0004921!1.27e-19!129;UBERON:0004185!1.27e-19!129;UBERON:0000062!3.54e-17!511;UBERON:0000481!6.34e-16!347;UBERON:0000077!1.10e-15!130;UBERON:0002346!3.30e-14!90;UBERON:0003075!4.28e-14!86;UBERON:0007284!4.28e-14!86;UBERON:0000153!5.01e-14!129;UBERON:0007811!5.01e-14!129;UBERON:0000033!7.20e-14!123;UBERON:0001049!2.37e-13!57;UBERON:0005068!2.37e-13!57;UBERON:0006241!2.37e-13!57;UBERON:0007135!2.37e-13!57;UBERON:0000477!5.86e-13!286;UBERON:0000924!7.34e-13!173;UBERON:0006601!7.34e-13!173;UBERON:0004121!1.28e-12!169;UBERON:0001041!4.25e-12!98;UBERON:0005743!9.43e-12!86;UBERON:0000073!1.36e-11!94;UBERON:0001016!1.36e-11!94;UBERON:0003056!5.40e-11!61;UBERON:0001017!5.43e-11!82;UBERON:0003080!5.69e-11!42;UBERON:0000064!7.07e-11!219;UBERON:0000468!7.66e-11!659;UBERON:0000922!9.17e-11!612;UBERON:0005911!9.29e-11!82;UBERON:0000955!1.02e-10!69;UBERON:0006238!1.02e-10!69;UBERON:0004111!1.54e-10!241;UBERON:0002616!1.56e-10!59;UBERON:0002780!1.77e-10!41;UBERON:0001890!1.77e-10!41;UBERON:0006240!1.77e-10!41;UBERON:0003929!6.89e-10!54;UBERON:0001048!8.24e-10!168;UBERON:0000467!9.63e-10!625;UBERON:0002050!1.25e-09!605;UBERON:0005423!1.25e-09!605;UBERON:0000480!1.40e-09!626;UBERON:0000923!1.96e-09!604;UBERON:0005291!1.96e-09!604;UBERON:0006598!1.96e-09!604;UBERON:0002532!1.96e-09!604;UBERON:0009497!9.16e-09!25;UBERON:0000015!9.16e-09!25;UBERON:0002423!9.16e-09!25;UBERON:0006235!9.16e-09!25;UBERON:0004161!9.16e-09!25;UBERON:0002530!1.96e-08!59;UBERON:0001004!2.40e-08!72;UBERON:0000161!3.71e-08!35;UBERON:0000475!5.89e-08!365;UBERON:0002020!6.52e-08!34;UBERON:0003528!6.52e-08!34;UBERON:0001893!1.04e-07!34;UBERON:0002791!1.76e-07!33;UBERON:0005409!1.86e-07!35;UBERON:0009854!2.10e-07!23;UBERON:0001869!3.86e-07!32;UBERON:0008835!4.03e-07!22;UBERON:0003894!4.03e-07!22;UBERON:0000483!5.07e-07!309;UBERON:0000466!7.35e-07!126;UBERON:0009856!8.75e-07!26;UBERON:0000119!9.20e-07!312
|ontology_enrichment_uberon=UBERON:0007023!1.08e-34!115;UBERON:0001007!3.93e-22!155;UBERON:0001555!3.93e-22!155;UBERON:0007026!3.93e-22!155;UBERON:0004119!7.44e-21!169;UBERON:0000925!7.44e-21!169;UBERON:0006595!7.44e-21!169;UBERON:0004921!1.27e-19!129;UBERON:0004185!1.27e-19!129;UBERON:0000062!3.54e-17!511;UBERON:0000481!6.34e-16!347;UBERON:0000077!1.10e-15!130;UBERON:0002346!3.30e-14!90;UBERON:0003075!4.28e-14!86;UBERON:0007284!4.28e-14!86;UBERON:0000153!5.01e-14!129;UBERON:0007811!5.01e-14!129;UBERON:0000033!7.20e-14!123;UBERON:0001049!2.37e-13!57;UBERON:0005068!2.37e-13!57;UBERON:0006241!2.37e-13!57;UBERON:0007135!2.37e-13!57;UBERON:0000477!5.86e-13!286;UBERON:0000924!7.34e-13!173;UBERON:0006601!7.34e-13!173;UBERON:0004121!1.28e-12!169;UBERON:0001041!4.25e-12!98;UBERON:0005743!9.43e-12!86;UBERON:0000073!1.36e-11!94;UBERON:0001016!1.36e-11!94;UBERON:0003056!5.40e-11!61;UBERON:0001017!5.43e-11!82;UBERON:0003080!5.69e-11!42;UBERON:0000064!7.07e-11!219;UBERON:0000468!7.66e-11!659;UBERON:0000922!9.17e-11!612;UBERON:0005911!9.29e-11!82;UBERON:0000955!1.02e-10!69;UBERON:0006238!1.02e-10!69;UBERON:0004111!1.54e-10!241;UBERON:0002616!1.56e-10!59;UBERON:0002780!1.77e-10!41;UBERON:0001890!1.77e-10!41;UBERON:0006240!1.77e-10!41;UBERON:0003929!6.89e-10!54;UBERON:0001048!8.24e-10!168;UBERON:0000467!9.63e-10!625;UBERON:0002050!1.25e-09!605;UBERON:0005423!1.25e-09!605;UBERON:0000480!1.40e-09!626;UBERON:0000923!1.96e-09!604;UBERON:0005291!1.96e-09!604;UBERON:0006598!1.96e-09!604;UBERON:0002532!1.96e-09!604;UBERON:0009497!9.16e-09!25;UBERON:0000015!9.16e-09!25;UBERON:0002423!9.16e-09!25;UBERON:0006235!9.16e-09!25;UBERON:0004161!9.16e-09!25;UBERON:0002530!1.96e-08!59;UBERON:0001004!2.40e-08!72;UBERON:0000161!3.71e-08!35;UBERON:0000475!5.89e-08!365;UBERON:0002020!6.52e-08!34;UBERON:0003528!6.52e-08!34;UBERON:0001893!1.04e-07!34;UBERON:0002791!1.76e-07!33;UBERON:0005409!1.86e-07!35;UBERON:0009854!2.10e-07!23;UBERON:0001869!3.86e-07!32;UBERON:0008835!4.03e-07!22;UBERON:0003894!4.03e-07!22;UBERON:0000483!5.07e-07!309;UBERON:0000466!7.35e-07!126;UBERON:0009856!8.75e-07!26;UBERON:0000119!9.20e-07!312
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}}
}}

Revision as of 13:58, 5 September 2012


Full id: C4738_signet_lung_Intestinal_hepatoma_Hepatocyte_Prostate_pineal



Phase1 CAGE Peaks

Hg19::chr8:17658596..17658611,-p2@MTUS1
Hg19::chr8:17658625..17658646,-p4@MTUS1
Hg19::chr8:17658681..17658691,-p11@MTUS1


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
epithelial cell1.71e-14254
endodermal cell1.78e-1059
Uber Anatomy
Ontology termp-valuen
adult organism1.08e-34115
digestive system3.93e-22155
digestive tract3.93e-22155
primitive gut3.93e-22155
endoderm-derived structure7.44e-21169
endoderm7.44e-21169
presumptive endoderm7.44e-21169
subdivision of digestive tract1.27e-19129
endodermal part of digestive tract1.27e-19129
organ3.54e-17511
multi-tissue structure6.34e-16347
mixed endoderm/mesoderm-derived structure1.10e-15130
neurectoderm3.30e-1490
neural plate4.28e-1486
presumptive neural plate4.28e-1486
anterior region of body5.01e-14129
craniocervical region5.01e-14129
head7.20e-14123
neural tube2.37e-1357
neural rod2.37e-1357
future spinal cord2.37e-1357
neural keel2.37e-1357
anatomical cluster5.86e-13286
ectoderm7.34e-13173
presumptive ectoderm7.34e-13173
ectoderm-derived structure1.28e-12169
foregut4.25e-1298
regional part of nervous system1.36e-1194
nervous system1.36e-1194
pre-chordal neural plate5.40e-1161
central nervous system5.43e-1182
anterior neural tube5.69e-1142
organ part7.07e-11219
multi-cellular organism7.66e-11659
embryo9.17e-11612
endo-epithelium9.29e-1182
brain1.02e-1069
future brain1.02e-1069
anatomical conduit1.54e-10241
regional part of brain1.56e-1059
regional part of forebrain1.77e-1041
forebrain1.77e-1041
future forebrain1.77e-1041
gut epithelium6.89e-1054
primordium8.24e-10168
anatomical system9.63e-10625
embryonic structure1.25e-09605
developing anatomical structure1.25e-09605
anatomical group1.40e-09626
germ layer1.96e-09604
embryonic tissue1.96e-09604
presumptive structure1.96e-09604
epiblast (generic)1.96e-09604
epithelium of foregut-midgut junction9.16e-0925
anatomical boundary9.16e-0925
hepatobiliary system9.16e-0925
foregut-midgut junction9.16e-0925
septum transversum9.16e-0925
gland1.96e-0859
respiratory system2.40e-0872
orifice3.71e-0835
organism subdivision5.89e-08365
gray matter6.52e-0834
brain grey matter6.52e-0834
telencephalon1.04e-0734
regional part of telencephalon1.76e-0733
gastrointestinal system1.86e-0735
digestive tract diverticulum2.10e-0723
cerebral hemisphere3.86e-0732
hepatic diverticulum4.03e-0722
liver primordium4.03e-0722
epithelium5.07e-07309
immaterial anatomical entity7.35e-07126
sac8.75e-0726
cell layer9.20e-07312
Disease
Ontology termp-valuen
carcinoma2.49e-25106
cell type cancer1.26e-24143
cancer3.51e-12235
disease of cellular proliferation5.02e-11239
adenocarcinoma9.79e-0825


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
E2F1#186934.907389214879320.008460985347239390.0327875347363858
E2F4#1874312.66806031528440.0004917987006298980.00439074752052368
EP300#203336.77394172622320.003216880500103790.0168548528846807
FOXA1#3169311.08141974938550.000734755275698670.00584352012174028
FOXA2#3170324.63046375266526.68983856509345e-050.00107721253453561
HDAC2#3066313.41562023662630.0004140761399857210.00393679544687926
HNF4A#3172323.13229036295378.07584663437677e-050.00123489509026014
HNF4G#3174328.75342252644684.20470658818262e-050.000760802757039509
NR3C1#2908314.9730233311730.0002978331194675480.00310371115187301
RXRA#6256320.07461713913330.0001235730348432220.00166034274874454
SP1#666735.69838137814090.005403962701712170.0247993874946883
STAT3#6774310.51946499715420.0008589184530415310.00645914345601991
TCF7L2#6934310.77017656313730.0008003181298398380.00617679760289262
TFAP2A#7020316.5186343730450.0002218033880766340.00249541355675273
TFAP2C#7022310.80922860986020.0007916746575753130.006190604190065



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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