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Coexpression cluster:C4329: Difference between revisions

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|full_id=C4329_mesenchymal_epithelioid_meningioma_Smooth_embryonic_Bronchial_Gingival
|full_id=C4329_mesenchymal_epithelioid_meningioma_Smooth_embryonic_Bronchial_Gingival
|id=C4329
|id=C4329
|ontology_enrichment_celltype=CL:0002321!2.53e-22!248;CL:0000220!2.99e-22!246;CL:0000066!1.20e-21!254;CL:0000680!1.21e-14!57;CL:0000056!1.21e-14!57;CL:0000355!1.21e-14!57;CL:0000192!1.41e-14!42;CL:0000514!1.41e-14!42;CL:0000187!1.92e-14!54;CL:0000393!2.23e-14!60;CL:0000211!2.23e-14!60;CL:0000183!2.33e-14!59;CL:0002076!1.90e-13!43;CL:0000359!1.73e-12!32;CL:0000548!3.80e-10!679;CL:0000004!3.80e-10!679;CL:0000255!3.80e-10!679;CL:0000012!4.42e-10!682;CL:0000222!8.19e-10!119;CL:0000223!1.40e-08!59;CL:0002368!2.21e-07!13;CL:0002539!2.90e-07!10;CL:0000055!5.43e-07!180
|ontology_enrichment_celltype=CL:0002321!4.51e-23!250;CL:0000066!1.76e-17!253;CL:0000680!6.57e-16!58;CL:0000056!6.57e-16!58;CL:0000355!6.57e-16!58;CL:0000192!1.10e-15!43;CL:0000514!1.10e-15!43;CL:0000187!1.42e-15!55;CL:0000393!1.47e-15!61;CL:0000211!1.47e-15!61;CL:0000183!1.50e-15!59;CL:0002076!5.91e-14!42;CL:0000359!3.32e-13!32;CL:0000222!1.40e-10!121;CL:0000548!1.52e-09!679;CL:0000255!1.52e-09!679;CL:0000223!7.20e-09!58;CL:0002539!9.78e-08!10;CL:0002368!5.38e-07!13;CL:0000055!7.97e-07!106
|ontology_enrichment_disease=DOID:193!1.35e-11!29;DOID:120!3.53e-11!27;DOID:2394!1.01e-09!14;DOID:305!3.42e-09!106
|ontology_enrichment_disease=DOID:193!1.82e-11!29;DOID:120!4.86e-11!27;DOID:2394!1.16e-09!14;DOID:305!1.83e-07!106
|ontology_enrichment_uberon=UBERON:0003104!2.96e-19!238;UBERON:0009142!2.96e-19!238;UBERON:0000481!1.04e-18!347;UBERON:0000486!1.69e-16!82;UBERON:0000467!3.67e-16!625;UBERON:0005256!4.07e-16!143;UBERON:0000922!7.00e-16!612;UBERON:0000480!7.72e-16!626;UBERON:0002050!2.88e-15!605;UBERON:0005423!2.88e-15!605;UBERON:0000923!4.18e-15!604;UBERON:0005291!4.18e-15!604;UBERON:0006598!4.18e-15!604;UBERON:0002532!4.18e-15!604;UBERON:0002100!9.78e-15!216;UBERON:0004119!2.36e-14!169;UBERON:0000925!2.36e-14!169;UBERON:0006595!2.36e-14!169;UBERON:0000483!4.34e-14!309;UBERON:0004290!5.37e-14!70;UBERON:0000119!6.19e-14!312;UBERON:0000468!2.47e-13!659;UBERON:0000914!4.28e-13!83;UBERON:0002329!4.28e-13!83;UBERON:0003077!4.28e-13!83;UBERON:0003059!4.28e-13!83;UBERON:0007282!4.28e-13!83;UBERON:0009618!4.28e-13!83;UBERON:0007285!4.28e-13!83;UBERON:0000464!1.14e-12!104;UBERON:0000926!3.01e-12!448;UBERON:0004120!3.01e-12!448;UBERON:0006603!3.01e-12!448;UBERON:0001637!3.89e-12!42;UBERON:0003509!3.89e-12!42;UBERON:0004572!3.89e-12!42;UBERON:0001134!3.93e-12!61;UBERON:0002036!3.93e-12!61;UBERON:0003082!3.93e-12!61;UBERON:0002385!6.05e-12!63;UBERON:0001015!6.05e-12!63;UBERON:0000383!6.05e-12!63;UBERON:0001007!1.36e-11!155;UBERON:0001555!1.36e-11!155;UBERON:0007026!1.36e-11!155;UBERON:0004573!1.46e-11!33;UBERON:0004571!1.46e-11!33;UBERON:0000490!2.13e-11!138;UBERON:0001048!3.59e-11!168;UBERON:0000466!3.75e-10!126;UBERON:0003914!2.12e-09!118;UBERON:0000475!5.23e-09!365;UBERON:0000062!6.41e-09!511;UBERON:0004921!1.26e-08!129;UBERON:0004185!1.26e-08!129;UBERON:0005156!5.44e-08!59;UBERON:0000990!5.44e-08!59;UBERON:0001004!8.53e-08!72;UBERON:0002553!8.67e-08!70;UBERON:0001981!1.22e-07!60;UBERON:0007500!1.22e-07!60;UBERON:0004537!1.22e-07!60;UBERON:0006965!1.22e-07!60;UBERON:0003886!1.66e-07!63;UBERON:0003100!2.72e-07!41;UBERON:0004237!2.90e-07!10;UBERON:0004695!2.90e-07!10;UBERON:0002111!2.90e-07!10;UBERON:0004178!2.90e-07!10;UBERON:0005153!4.93e-07!37;UBERON:0001135!6.38e-07!15;UBERON:0000058!9.22e-07!26
|ontology_enrichment_uberon=UBERON:0000475!4.04e-19!264;UBERON:0000486!5.26e-18!83;UBERON:0000467!2.83e-17!624;UBERON:0000480!5.50e-17!625;UBERON:0002329!1.08e-15!71;UBERON:0003059!1.08e-15!71;UBERON:0007282!1.08e-15!71;UBERON:0004290!1.08e-15!71;UBERON:0009618!1.08e-15!71;UBERON:0002100!2.39e-15!199;UBERON:0003077!2.54e-15!72;UBERON:0007285!2.54e-15!72;UBERON:0007503!2.90e-15!78;UBERON:0000481!5.63e-15!342;UBERON:0000922!6.00e-15!592;UBERON:0007524!1.17e-14!73;UBERON:0005256!2.06e-14!122;UBERON:0000490!3.69e-14!148;UBERON:0000468!4.89e-14!656;UBERON:0000483!1.45e-13!306;UBERON:0001134!2.45e-13!62;UBERON:0002036!2.45e-13!62;UBERON:0003082!2.45e-13!62;UBERON:0000119!2.51e-13!309;UBERON:0001637!3.26e-13!42;UBERON:0003509!3.26e-13!42;UBERON:0004572!3.26e-13!42;UBERON:0005423!5.22e-13!581;UBERON:0002385!7.87e-13!64;UBERON:0001015!7.87e-13!64;UBERON:0000383!7.87e-13!64;UBERON:0003104!2.08e-12!160;UBERON:0009142!2.08e-12!160;UBERON:0004573!2.67e-12!33;UBERON:0004571!2.67e-12!33;UBERON:0002050!1.44e-11!564;UBERON:0004119!5.42e-11!160;UBERON:0000925!5.42e-11!160;UBERON:0006595!5.42e-11!160;UBERON:0000923!1.17e-10!560;UBERON:0010316!1.17e-10!560;UBERON:0005291!1.17e-10!560;UBERON:0006598!1.17e-10!560;UBERON:0010317!1.17e-10!560;UBERON:0002532!1.17e-10!560;UBERON:0003914!3.76e-09!117;UBERON:0001007!6.33e-09!145;UBERON:0001555!6.33e-09!145;UBERON:0007026!6.33e-09!145;UBERON:0000464!6.36e-09!95;UBERON:0000062!9.88e-09!503;UBERON:0007500!2.22e-08!59;UBERON:0001981!2.22e-08!59;UBERON:0004537!2.22e-08!59;UBERON:0006965!2.22e-08!59;UBERON:0000477!9.16e-08!373;UBERON:0004237!9.78e-08!10;UBERON:0004695!9.78e-08!10;UBERON:0002111!9.78e-08!10;UBERON:0004178!9.78e-08!10;UBERON:0003102!1.11e-07!99;UBERON:0001048!3.27e-07!160;UBERON:0005156!4.65e-07!59;UBERON:0000990!4.65e-07!59;UBERON:0001135!5.29e-07!15;UBERON:0000466!6.10e-07!117;UBERON:0001004!6.42e-07!74
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190666296495866!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326723673992581!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472485167537174!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010974903536342
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190666296495866!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326723673992581!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472485167537174!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010974903536342
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}}
}}

Revision as of 15:52, 19 October 2012


Full id: C4329_mesenchymal_epithelioid_meningioma_Smooth_embryonic_Bronchial_Gingival



Phase1 CAGE Peaks

Hg19::chr3:45187813..45187824,-p3@CDCP1
Hg19::chr3:45187843..45187907,-p1@CDCP1
Hg19::chr3:45187930..45187949,-p2@CDCP1


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>

Uber Anatomy
Ontology termp-valuen
organism subdivision4.04e-19264
multilaminar epithelium5.26e-1883
anatomical system2.83e-17624
anatomical group5.50e-17625
somite1.08e-1571
presomitic mesoderm1.08e-1571
presumptive segmental plate1.08e-1571
dermomyotome1.08e-1571
trunk paraxial mesoderm1.08e-1571
trunk2.39e-15199
paraxial mesoderm2.54e-1572
presumptive paraxial mesoderm2.54e-1572
epithelial vesicle2.90e-1578
multi-tissue structure5.63e-15342
embryo6.00e-15592
dense mesenchyme tissue1.17e-1473
trunk mesenchyme2.06e-14122
unilaminar epithelium3.69e-14148
multi-cellular organism4.89e-14656
epithelium1.45e-13306
skeletal muscle tissue2.45e-1362
striated muscle tissue2.45e-1362
myotome2.45e-1362
cell layer2.51e-13309
artery3.26e-1342
arterial blood vessel3.26e-1342
arterial system3.26e-1342
developing anatomical structure5.22e-13581
muscle tissue7.87e-1364
musculature7.87e-1364
musculature of body7.87e-1364
mesenchyme2.08e-12160
entire embryonic mesenchyme2.08e-12160
systemic artery2.67e-1233
systemic arterial system2.67e-1233
embryonic structure1.44e-11564
endoderm-derived structure5.42e-11160
endoderm5.42e-11160
presumptive endoderm5.42e-11160
germ layer1.17e-10560
germ layer / neural crest1.17e-10560
embryonic tissue1.17e-10560
presumptive structure1.17e-10560
germ layer / neural crest derived structure1.17e-10560
epiblast (generic)1.17e-10560
epithelial tube3.76e-09117
digestive system6.33e-09145
digestive tract6.33e-09145
primitive gut6.33e-09145
anatomical space6.36e-0995
organ9.88e-09503
epithelial tube open at both ends2.22e-0859
blood vessel2.22e-0859
blood vasculature2.22e-0859
vascular cord2.22e-0859
anatomical cluster9.16e-08373
blood vessel smooth muscle9.78e-0810
arterial system smooth muscle9.78e-0810
artery smooth muscle tissue9.78e-0810
aorta smooth muscle tissue9.78e-0810
surface structure1.11e-0799
primordium3.27e-07160
reproductive structure4.65e-0759
reproductive system4.65e-0759
smooth muscle tissue5.29e-0715
immaterial anatomical entity6.10e-07117
respiratory system6.42e-0774
Disease
Ontology termp-valuen
reproductive organ cancer1.82e-1129
female reproductive organ cancer4.86e-1127
ovarian cancer1.16e-0914
carcinoma1.83e-07106


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
CCNT2#90536.336201576962630.003930750035764890.0190666296495866
E2F1#186934.907389214879320.008460985347239390.0326723673992581
NRF1#4899312.21027944771090.0005492172401020010.00472485167537174
ZNF263#1012738.221841637010680.001799043925565870.010974903536342



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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