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Coexpression cluster:C2874: Difference between revisions

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|full_id=C2874_mature_neuroblastoma_oral_pharyngeal_normal_neuroectodermal_mesothelioma
|full_id=C2874_mature_neuroblastoma_oral_pharyngeal_normal_neuroectodermal_mesothelioma
|id=C2874
|id=C2874
|ontology_enrichment_celltype=CL:0000066!5.60e-19!254;CL:0000220!2.64e-18!246;CL:0002321!1.09e-17!248;CL:0000076!7.37e-16!62;CL:0000222!6.73e-14!119;CL:0002139!3.56e-12!24;CL:0000213!2.16e-11!57;CL:0000215!2.16e-11!57;CL:0000057!2.01e-09!75;CL:0000115!3.00e-09!35;CL:0000071!7.16e-09!18;CL:0002546!7.16e-09!18;CL:0000055!1.72e-08!180;CL:0002078!5.35e-08!44;CL:0002076!1.07e-07!43;CL:0000136!1.45e-07!15
|ontology_enrichment_celltype=CL:0000066!5.73e-19!253;CL:0002321!7.13e-19!250;CL:0000076!2.48e-16!63;CL:0000222!2.12e-14!121;CL:0002139!1.79e-12!24;CL:0000213!3.88e-12!58;CL:0000215!3.88e-12!58;CL:0000115!4.12e-10!36;CL:0000057!1.23e-09!76;CL:0000071!3.99e-09!18;CL:0002546!3.99e-09!18;CL:0002078!1.21e-08!45;CL:0002076!9.73e-08!42;CL:0000136!1.43e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!9.40e-15!659;UBERON:0000055!1.71e-12!69;UBERON:0002049!2.89e-12!79;UBERON:0007798!2.89e-12!79;UBERON:0002100!3.21e-12!216;UBERON:0000467!4.69e-12!625;UBERON:0004872!5.16e-12!84;UBERON:0000480!5.72e-12!626;UBERON:0000119!8.41e-12!312;UBERON:0000483!1.13e-11!309;UBERON:0000475!1.35e-11!365;UBERON:0003102!1.69e-11!95;UBERON:0003914!4.28e-11!118;UBERON:0004923!1.09e-10!57;UBERON:0000490!1.36e-10!138;UBERON:0000477!4.30e-10!286;UBERON:0003104!7.19e-10!238;UBERON:0009142!7.19e-10!238;UBERON:0001981!9.25e-10!60;UBERON:0007500!9.25e-10!60;UBERON:0004537!9.25e-10!60;UBERON:0006965!9.25e-10!60;UBERON:0001009!2.62e-09!113;UBERON:0004111!2.67e-09!241;UBERON:0000481!2.75e-09!347;UBERON:0005256!3.42e-09!143;UBERON:0000487!4.13e-09!22;UBERON:0004119!4.23e-09!169;UBERON:0000925!4.23e-09!169;UBERON:0006595!4.23e-09!169;UBERON:0001986!7.16e-09!18;UBERON:0004638!7.16e-09!18;UBERON:0004852!7.16e-09!18;UBERON:0004535!1.48e-08!110;UBERON:0000486!6.15e-08!82;UBERON:0005631!6.41e-08!14;UBERON:0000158!6.41e-08!14;UBERON:0006914!1.28e-07!25;UBERON:0000064!1.93e-07!219;UBERON:0002199!5.42e-07!45;UBERON:0002416!5.42e-07!45;UBERON:0000914!5.79e-07!83;UBERON:0002329!5.79e-07!83;UBERON:0003077!5.79e-07!83;UBERON:0003059!5.79e-07!83;UBERON:0007282!5.79e-07!83;UBERON:0009618!5.79e-07!83;UBERON:0007285!5.79e-07!83;UBERON:0002050!8.37e-07!605;UBERON:0005423!8.37e-07!605
|ontology_enrichment_uberon=UBERON:0000468!3.09e-15!656;UBERON:0000475!5.47e-14!264;UBERON:0003102!4.60e-13!99;UBERON:0000055!7.79e-13!68;UBERON:0002049!1.43e-12!78;UBERON:0007798!1.43e-12!78;UBERON:0000490!1.79e-12!148;UBERON:0000467!2.47e-12!624;UBERON:0000480!3.08e-12!625;UBERON:0000119!4.70e-12!309;UBERON:0004872!6.72e-12!83;UBERON:0000483!6.98e-12!306;UBERON:0004923!1.40e-11!66;UBERON:0003914!2.32e-11!117;UBERON:0002100!7.46e-11!199;UBERON:0007500!5.88e-10!59;UBERON:0001981!5.88e-10!59;UBERON:0004537!5.88e-10!59;UBERON:0006965!5.88e-10!59;UBERON:0000477!1.24e-09!373;UBERON:0001009!2.75e-09!112;UBERON:0000487!2.77e-09!22;UBERON:0004119!2.90e-09!160;UBERON:0000925!2.90e-09!160;UBERON:0006595!2.90e-09!160;UBERON:0004638!3.99e-09!18;UBERON:0001986!3.99e-09!18;UBERON:0004852!3.99e-09!18;UBERON:0004111!4.86e-09!240;UBERON:0004535!1.72e-08!109;UBERON:0000481!1.87e-08!342;UBERON:0000486!4.93e-08!83;UBERON:0005256!6.41e-08!122;UBERON:0006914!7.93e-08!25;UBERON:0005631!8.61e-08!14;UBERON:0000158!8.61e-08!14;UBERON:0002199!3.20e-07!46;UBERON:0002416!3.20e-07!46;UBERON:0002050!3.56e-07!564;UBERON:0000064!3.66e-07!218;UBERON:0005423!7.03e-07!581;UBERON:0007503!7.81e-07!78
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051363325317388!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186596405670175!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387191590548422!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107075416933143!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347274429612611
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051363325317388!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186596405670175!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387191590548422!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107075416933143!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347274429612611
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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2874_mature_neuroblastoma_oral_pharyngeal_normal_neuroectodermal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr7:116139649..116139711,+p2@CAV2
Hg19::chr7:116139744..116139818,+p1@CAV2
Hg19::chr7:116139821..116139832,+p3@CAV2
Hg19::chr7:116140090..116140138,+p4@CAV2


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
multi-cellular organism3.09e-15656
organism subdivision5.47e-14264
surface structure4.60e-1399
vessel7.79e-1368
vasculature1.43e-1278
vascular system1.43e-1278
unilaminar epithelium1.79e-12148
anatomical system2.47e-12624
anatomical group3.08e-12625
cell layer4.70e-12309
splanchnic layer of lateral plate mesoderm6.72e-1283
epithelium6.98e-12306
organ component layer1.40e-1166
epithelial tube2.32e-11117
trunk7.46e-11199
epithelial tube open at both ends5.88e-1059
blood vessel5.88e-1059
blood vasculature5.88e-1059
vascular cord5.88e-1059
anatomical cluster1.24e-09373
circulatory system2.75e-09112
simple squamous epithelium2.77e-0922
endoderm-derived structure2.90e-09160
endoderm2.90e-09160
presumptive endoderm2.90e-09160
blood vessel endothelium3.99e-0918
endothelium3.99e-0918
cardiovascular system endothelium3.99e-0918
anatomical conduit4.86e-09240
cardiovascular system1.72e-08109
multi-tissue structure1.87e-08342
multilaminar epithelium4.93e-0883
trunk mesenchyme6.41e-08122
squamous epithelium7.93e-0825
extraembryonic membrane8.61e-0814
membranous layer8.61e-0814
integument3.20e-0746
integumental system3.20e-0746
embryonic structure3.56e-07564
organ part3.66e-07218
developing anatomical structure7.03e-07581
epithelial vesicle7.81e-0778


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#90546.336201576962630.0006203100587215640.0051363325317388
HEY1#2346244.040111043105710.00375304636917980.0186596405670175
JUND#372735.245997956403270.01043432751748420.0387191590548422
YY1#752844.911170749853860.00171871838055440.0107075416933143
ZBTB7A#5134147.35190930787590.000342223540015990.00347274429612611



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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