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Coexpression cluster:C4677: Difference between revisions

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|full_id=C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial
|full_id=C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial
|id=C4677
|id=C4677
|ontology_enrichment_celltype=CL:0000222!1.74e-26!119;CL:0000076!6.70e-14!62;CL:0000213!1.21e-13!57;CL:0000215!1.21e-13!57;CL:0000187!9.61e-13!54;CL:0000183!1.42e-12!59;CL:0000680!1.73e-12!57;CL:0000056!1.73e-12!57;CL:0000355!1.73e-12!57;CL:0002139!3.01e-11!24;CL:0000192!1.67e-10!42;CL:0000514!1.67e-10!42;CL:0002078!4.53e-10!44;CL:0000115!1.01e-09!35;CL:0000393!1.12e-09!60;CL:0000211!1.12e-09!60;CL:0000220!1.35e-09!246;CL:0000071!1.48e-09!18;CL:0002546!1.48e-09!18;CL:0002321!3.31e-09!248;CL:0000359!3.01e-07!32;CL:0000066!5.40e-07!254
|ontology_enrichment_celltype=CL:0000222!4.70e-28!121;CL:0000213!1.44e-14!58;CL:0000215!1.44e-14!58;CL:0000187!6.42e-14!55;CL:0000076!9.38e-14!63;CL:0000183!4.05e-13!59;CL:0000680!6.30e-13!58;CL:0000056!6.30e-13!58;CL:0000355!6.30e-13!58;CL:0000192!3.77e-12!43;CL:0000514!3.77e-12!43;CL:0002321!3.61e-11!250;CL:0000393!5.72e-11!61;CL:0000211!5.72e-11!61;CL:0002078!1.51e-10!45;CL:0002139!5.82e-10!24;CL:0000115!7.57e-10!36;CL:0000071!1.05e-08!18;CL:0002546!1.05e-08!18;CL:0000359!1.02e-07!32;CL:0000077!3.17e-07!19;CL:0000066!7.26e-07!253
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002100!5.12e-22!216;UBERON:0003104!3.42e-21!238;UBERON:0009142!3.42e-21!238;UBERON:0000055!6.20e-21!69;UBERON:0003914!2.60e-20!118;UBERON:0001981!1.97e-18!60;UBERON:0007500!1.97e-18!60;UBERON:0004537!1.97e-18!60;UBERON:0006965!1.97e-18!60;UBERON:0000490!2.44e-18!138;UBERON:0005256!7.13e-17!143;UBERON:0002049!9.77e-16!79;UBERON:0007798!9.77e-16!79;UBERON:0000926!1.16e-14!448;UBERON:0004120!1.16e-14!448;UBERON:0006603!1.16e-14!448;UBERON:0004872!1.27e-14!84;UBERON:0005177!5.37e-14!107;UBERON:0002385!2.37e-13!63;UBERON:0001015!2.37e-13!63;UBERON:0000383!2.37e-13!63;UBERON:0004111!8.35e-13!241;UBERON:0001134!1.00e-12!61;UBERON:0002036!1.00e-12!61;UBERON:0003082!1.00e-12!61;UBERON:0001637!1.79e-12!42;UBERON:0003509!1.79e-12!42;UBERON:0004572!1.79e-12!42;UBERON:0003064!4.77e-12!37;UBERON:0009569!1.79e-11!113;UBERON:0000466!2.33e-11!126;UBERON:0004921!5.86e-11!129;UBERON:0004185!5.86e-11!129;UBERON:0000464!9.41e-11!104;UBERON:0003886!1.09e-10!63;UBERON:0004290!3.47e-10!70;UBERON:0000481!3.68e-10!347;UBERON:0001008!9.63e-10!45;UBERON:0000477!9.94e-10!286;UBERON:0000483!1.46e-09!309;UBERON:0001986!1.48e-09!18;UBERON:0004638!1.48e-09!18;UBERON:0004852!1.48e-09!18;UBERON:0004573!1.93e-09!33;UBERON:0004571!1.93e-09!33;UBERON:0006554!3.20e-09!44;UBERON:0002553!3.92e-09!70;UBERON:0000119!4.93e-09!312;UBERON:0000025!6.16e-09!194;UBERON:0000487!9.39e-09!22;UBERON:0001009!1.33e-08!113;UBERON:0002417!1.44e-08!61;UBERON:0000916!1.44e-08!61;UBERON:0000947!1.83e-08!21;UBERON:0010191!1.83e-08!21;UBERON:0004535!1.95e-08!110;UBERON:0001007!2.66e-08!155;UBERON:0001555!2.66e-08!155;UBERON:0007026!2.66e-08!155;UBERON:0000489!2.70e-08!32;UBERON:0005172!4.15e-08!55;UBERON:0005173!4.15e-08!55;UBERON:0005156!7.39e-08!59;UBERON:0000990!7.39e-08!59;UBERON:0000486!9.29e-08!82;UBERON:0000077!1.11e-07!130;UBERON:0004119!2.04e-07!169;UBERON:0000925!2.04e-07!169;UBERON:0006595!2.04e-07!169;UBERON:0006914!3.04e-07!25;UBERON:0000475!4.62e-07!365;UBERON:0005409!5.33e-07!35;UBERON:0000080!7.29e-07!18;UBERON:0002120!7.29e-07!18;UBERON:0004875!7.29e-07!18;UBERON:0005721!7.29e-07!18;UBERON:0005754!7.29e-07!18;UBERON:0007297!7.29e-07!18;UBERON:0000914!7.37e-07!83;UBERON:0002329!7.37e-07!83;UBERON:0003077!7.37e-07!83;UBERON:0003059!7.37e-07!83;UBERON:0007282!7.37e-07!83;UBERON:0009618!7.37e-07!83;UBERON:0007285!7.37e-07!83;UBERON:0002113!8.46e-07!27;UBERON:0003918!8.46e-07!27;UBERON:0005095!8.46e-07!27;UBERON:0007687!8.46e-07!27
|ontology_enrichment_uberon=UBERON:0002100!7.70e-25!199;UBERON:0003104!4.62e-24!160;UBERON:0009142!4.62e-24!160;UBERON:0000055!3.53e-20!68;UBERON:0005256!1.79e-19!122;UBERON:0007500!4.84e-18!59;UBERON:0001981!4.84e-18!59;UBERON:0004537!4.84e-18!59;UBERON:0006965!4.84e-18!59;UBERON:0003914!5.13e-18!117;UBERON:0000490!3.49e-17!148;UBERON:0002049!1.20e-15!78;UBERON:0007798!1.20e-15!78;UBERON:0000475!1.46e-15!264;UBERON:0005177!4.75e-14!101;UBERON:0002385!8.48e-14!64;UBERON:0001015!8.48e-14!64;UBERON:0000383!8.48e-14!64;UBERON:0001134!3.04e-13!62;UBERON:0002036!3.04e-13!62;UBERON:0003082!3.04e-13!62;UBERON:0007503!2.83e-12!78;UBERON:0004111!3.69e-12!240;UBERON:0004872!3.91e-12!83;UBERON:0001637!5.87e-12!42;UBERON:0003509!5.87e-12!42;UBERON:0004572!5.87e-12!42;UBERON:0000477!7.39e-12!373;UBERON:0009569!1.05e-11!112;UBERON:0003064!1.82e-10!28;UBERON:0002329!2.39e-10!71;UBERON:0003059!2.39e-10!71;UBERON:0007282!2.39e-10!71;UBERON:0004290!2.39e-10!71;UBERON:0009618!2.39e-10!71;UBERON:0000466!3.44e-10!117;UBERON:0003077!5.57e-10!72;UBERON:0007285!5.57e-10!72;UBERON:0007524!1.26e-09!73;UBERON:0004921!1.92e-09!118;UBERON:0000483!2.08e-09!306;UBERON:0000464!2.14e-09!95;UBERON:0001008!3.87e-09!48;UBERON:0000119!5.93e-09!309;UBERON:0000481!8.13e-09!342;UBERON:0004638!1.05e-08!18;UBERON:0001986!1.05e-08!18;UBERON:0004852!1.05e-08!18;UBERON:0006554!1.41e-08!47;UBERON:0000489!1.78e-08!31;UBERON:0004573!1.80e-08!33;UBERON:0004571!1.80e-08!33;UBERON:0000025!2.28e-08!192;UBERON:0005172!2.62e-08!54;UBERON:0005173!2.62e-08!54;UBERON:0000487!2.97e-08!22;UBERON:0003886!3.24e-08!54;UBERON:0000926!3.83e-08!315;UBERON:0004120!3.83e-08!315;UBERON:0006603!3.83e-08!315;UBERON:0002417!4.81e-08!60;UBERON:0000916!4.81e-08!60;UBERON:0000486!5.01e-08!83;UBERON:0005156!5.09e-08!59;UBERON:0000990!5.09e-08!59;UBERON:0004535!1.85e-07!109;UBERON:0001007!2.67e-07!145;UBERON:0001555!2.67e-07!145;UBERON:0007026!2.67e-07!145;UBERON:0001009!3.53e-07!112;UBERON:0006914!5.04e-07!25;UBERON:0002553!7.64e-07!61;UBERON:0000947!7.99e-07!21;UBERON:0010191!7.99e-07!21;UBERON:0000162!8.79e-07!14;UBERON:0001353!8.79e-07!14;UBERON:0000163!8.79e-07!14;UBERON:0006866!8.79e-07!14;UBERON:0000164!8.79e-07!14;UBERON:0000931!8.79e-07!14
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.00013053491124993!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901808439836254!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438982631773451!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645496037398032!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223409654780876!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617269220606623!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331210892795519!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110122112614098
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.00013053491124993!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901808439836254!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438982631773451!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645496037398032!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223409654780876!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617269220606623!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331210892795519!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110122112614098
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}}
}}

Revision as of 16:09, 19 October 2012


Full id: C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial



Phase1 CAGE Peaks

Hg19::chr7:27153185..27153215,+p1@ENST00000522193
Hg19::chr7:27153226..27153257,+p2@ENST00000522193
Hg19::chr7:27153269..27153285,+p3@ENST00000522193


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><br>


Uber Anatomy
Ontology termp-valuen
trunk7.70e-25199
mesenchyme4.62e-24160
entire embryonic mesenchyme4.62e-24160
vessel3.53e-2068
trunk mesenchyme1.79e-19122
epithelial tube open at both ends4.84e-1859
blood vessel4.84e-1859
blood vasculature4.84e-1859
vascular cord4.84e-1859
epithelial tube5.13e-18117
unilaminar epithelium3.49e-17148
vasculature1.20e-1578
vascular system1.20e-1578
organism subdivision1.46e-15264
trunk region element4.75e-14101
muscle tissue8.48e-1464
musculature8.48e-1464
musculature of body8.48e-1464
skeletal muscle tissue3.04e-1362
striated muscle tissue3.04e-1362
myotome3.04e-1362
epithelial vesicle2.83e-1278
anatomical conduit3.69e-12240
splanchnic layer of lateral plate mesoderm3.91e-1283
artery5.87e-1242
arterial blood vessel5.87e-1242
arterial system5.87e-1242
anatomical cluster7.39e-12373
subdivision of trunk1.05e-11112
intermediate mesoderm1.82e-1028
somite2.39e-1071
presomitic mesoderm2.39e-1071
presumptive segmental plate2.39e-1071
dermomyotome2.39e-1071
trunk paraxial mesoderm2.39e-1071
immaterial anatomical entity3.44e-10117
paraxial mesoderm5.57e-1072
presumptive paraxial mesoderm5.57e-1072
dense mesenchyme tissue1.26e-0973
subdivision of digestive tract1.92e-09118
epithelium2.08e-09306
anatomical space2.14e-0995
renal system3.87e-0948
cell layer5.93e-09309
multi-tissue structure8.13e-09342
blood vessel endothelium1.05e-0818
endothelium1.05e-0818
cardiovascular system endothelium1.05e-0818
urinary system structure1.41e-0847
cavitated compound organ1.78e-0831
systemic artery1.80e-0833
systemic arterial system1.80e-0833
tube2.28e-08192
abdomen element2.62e-0854
abdominal segment element2.62e-0854
simple squamous epithelium2.97e-0822
body cavity precursor3.24e-0854
mesoderm3.83e-08315
mesoderm-derived structure3.83e-08315
presumptive mesoderm3.83e-08315
abdominal segment of trunk4.81e-0860
abdomen4.81e-0860
multilaminar epithelium5.01e-0883
reproductive structure5.09e-0859
reproductive system5.09e-0859
cardiovascular system1.85e-07109
digestive system2.67e-07145
digestive tract2.67e-07145
primitive gut2.67e-07145
circulatory system3.53e-07112
squamous epithelium5.04e-0725
anatomical cavity7.64e-0761
aorta7.99e-0721
aortic system7.99e-0721
cloaca8.79e-0714
anal region8.79e-0714
embryonic cloaca8.79e-0714
terminal part of digestive tract8.79e-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
CTBP2#1488362.71700033932814.049570681927e-060.00013053491124993
FOS#235338.99795530889440.001372499272417130.00901808439836254
GATA2#2624312.7449317335540.0004829527704283790.00438982631773451
STAT3#6774310.51946499715420.0008589184530415310.00645496037398032
SUZ12#23512350.11578091106297.93834897779404e-060.000223409654780876
TCF7L2#6934310.77017656313730.0008003181298398380.00617269220606623
YY1#752834.911170749853860.008441455341808260.0331210892795519
ZNF263#1012738.221841637010680.001799043925565870.0110122112614098



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.