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Coexpression cluster:C4738: Difference between revisions

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|full_id=C4738_signet_lung_Intestinal_hepatoma_Hepatocyte_Prostate_pineal
|full_id=C4738_signet_lung_Intestinal_hepatoma_Hepatocyte_Prostate_pineal
|id=C4738
|id=C4738
|ontology_enrichment_celltype=CL:0000066!1.71e-14!254;CL:0000223!1.78e-10!59
|ontology_enrichment_celltype=CL:0000066!7.48e-12!253;CL:0000223!1.41e-11!58;CL:0002251!9.80e-07!20
|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!6.92e-27!106;DOID:0050687!5.56e-26!143;DOID:162!1.79e-13!235;DOID:14566!2.11e-12!239;DOID:299!6.65e-08!25;DOID:1749!1.23e-07!14
|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!7.05e-36!114;UBERON:0011216!8.31e-28!223;UBERON:0001007!2.52e-21!145;UBERON:0001555!2.52e-21!145;UBERON:0007026!2.52e-21!145;UBERON:0004119!2.62e-20!160;UBERON:0000925!2.62e-20!160;UBERON:0006595!2.62e-20!160;UBERON:0004921!9.38e-20!118;UBERON:0000477!5.97e-19!373;UBERON:0000481!1.01e-15!342;UBERON:0000062!1.91e-13!503;UBERON:0001041!1.23e-12!87;UBERON:0001049!1.36e-12!56;UBERON:0005068!1.36e-12!56;UBERON:0006241!1.36e-12!56;UBERON:0007135!1.36e-12!56;UBERON:0002346!8.44e-12!86;UBERON:0003929!9.14e-12!54;UBERON:0003075!1.69e-11!82;UBERON:0007284!1.69e-11!82;UBERON:0000073!1.82e-11!53;UBERON:0002616!1.82e-11!53;UBERON:0005911!3.18e-11!82;UBERON:0004111!3.69e-10!240;UBERON:0010371!4.23e-10!104;UBERON:0002780!5.45e-10!41;UBERON:0001890!5.45e-10!41;UBERON:0003080!5.45e-10!41;UBERON:0006240!5.45e-10!41;UBERON:0001017!6.22e-10!81;UBERON:0001016!7.35e-10!89;UBERON:0000955!7.63e-10!68;UBERON:0006238!7.63e-10!68;UBERON:0009497!2.45e-09!25;UBERON:0000015!2.45e-09!25;UBERON:0002423!2.45e-09!25;UBERON:0006235!2.45e-09!25;UBERON:0004161!2.45e-09!25;UBERON:0001048!4.98e-09!160;UBERON:0004121!5.51e-09!171;UBERON:0000924!5.51e-09!171;UBERON:0006601!5.51e-09!171;UBERON:0003056!9.58e-09!61;UBERON:0000064!1.11e-08!218;UBERON:0002530!2.46e-08!59;UBERON:0000468!3.00e-08!656;UBERON:0000161!6.07e-08!36;UBERON:0009854!7.11e-08!23;UBERON:0008835!1.01e-07!22;UBERON:0003894!1.01e-07!22;UBERON:0003528!1.94e-07!34;UBERON:0002020!1.94e-07!34;UBERON:0000466!1.99e-07!117;UBERON:0000922!2.36e-07!592;UBERON:0001893!2.54e-07!34;UBERON:0005409!2.90e-07!25;UBERON:0001004!3.27e-07!74;UBERON:0001046!6.20e-07!19;UBERON:0005423!7.16e-07!581;UBERON:0002368!7.40e-07!35;UBERON:0000467!8.08e-07!624;UBERON:0001869!8.68e-07!32;UBERON:0009856!9.01e-07!26;UBERON:0002791!9.35e-07!32
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327875347363858!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439074752052368!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168548528846807!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584352012174028!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107721253453561!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393679544687926!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123489509026014!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000760802757039509!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310371115187301!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00166034274874454!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247993874946883!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645914345601991!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617679760289262!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00249541355675273!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.006190604190065
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}}
}}

Revision as of 16:12, 19 October 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 cell7.48e-12253
endodermal cell1.41e-1158
epithelial cell of alimentary canal9.80e-0720
Uber Anatomy
Ontology termp-valuen
adult organism7.05e-36114
organ system subdivision8.31e-28223
digestive system2.52e-21145
digestive tract2.52e-21145
primitive gut2.52e-21145
endoderm-derived structure2.62e-20160
endoderm2.62e-20160
presumptive endoderm2.62e-20160
subdivision of digestive tract9.38e-20118
anatomical cluster5.97e-19373
multi-tissue structure1.01e-15342
organ1.91e-13503
foregut1.23e-1287
neural tube1.36e-1256
neural rod1.36e-1256
future spinal cord1.36e-1256
neural keel1.36e-1256
neurectoderm8.44e-1286
gut epithelium9.14e-1254
neural plate1.69e-1182
presumptive neural plate1.69e-1182
regional part of nervous system1.82e-1153
regional part of brain1.82e-1153
endo-epithelium3.18e-1182
anatomical conduit3.69e-10240
ecto-epithelium4.23e-10104
regional part of forebrain5.45e-1041
forebrain5.45e-1041
anterior neural tube5.45e-1041
future forebrain5.45e-1041
central nervous system6.22e-1081
nervous system7.35e-1089
brain7.63e-1068
future brain7.63e-1068
epithelium of foregut-midgut junction2.45e-0925
anatomical boundary2.45e-0925
hepatobiliary system2.45e-0925
foregut-midgut junction2.45e-0925
septum transversum2.45e-0925
primordium4.98e-09160
ectoderm-derived structure5.51e-09171
ectoderm5.51e-09171
presumptive ectoderm5.51e-09171
pre-chordal neural plate9.58e-0961
organ part1.11e-08218
gland2.46e-0859
multi-cellular organism3.00e-08656
orifice6.07e-0836
digestive tract diverticulum7.11e-0823
hepatic diverticulum1.01e-0722
liver primordium1.01e-0722
brain grey matter1.94e-0734
gray matter1.94e-0734
immaterial anatomical entity1.99e-07117
embryo2.36e-07592
telencephalon2.54e-0734
gastrointestinal system2.90e-0725
respiratory system3.27e-0774
hindgut6.20e-0719
developing anatomical structure7.16e-07581
endocrine gland7.40e-0735
anatomical system8.08e-07624
cerebral hemisphere8.68e-0732
sac9.01e-0726
regional part of telencephalon9.35e-0732
Disease
Ontology termp-valuen
carcinoma6.92e-27106
cell type cancer5.56e-26143
cancer1.79e-13235
disease of cellular proliferation2.11e-12239
adenocarcinoma6.65e-0825
squamous cell carcinoma1.23e-0714


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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