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Coexpression cluster:C2874: Difference between revisions

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|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!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
|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 13:12, 5 September 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 organism9.40e-15659
vessel1.71e-1269
vasculature2.89e-1279
vascular system2.89e-1279
trunk3.21e-12216
anatomical system4.69e-12625
splanchnic layer of lateral plate mesoderm5.16e-1284
anatomical group5.72e-12626
cell layer8.41e-12312
epithelium1.13e-11309
organism subdivision1.35e-11365
surface structure1.69e-1195
epithelial tube4.28e-11118
organ component layer1.09e-1057
unilaminar epithelium1.36e-10138
anatomical cluster4.30e-10286
mesenchyme7.19e-10238
entire embryonic mesenchyme7.19e-10238
blood vessel9.25e-1060
epithelial tube open at both ends9.25e-1060
blood vasculature9.25e-1060
vascular cord9.25e-1060
circulatory system2.62e-09113
anatomical conduit2.67e-09241
multi-tissue structure2.75e-09347
trunk mesenchyme3.42e-09143
simple squamous epithelium4.13e-0922
endoderm-derived structure4.23e-09169
endoderm4.23e-09169
presumptive endoderm4.23e-09169
endothelium7.16e-0918
blood vessel endothelium7.16e-0918
cardiovascular system endothelium7.16e-0918
cardiovascular system1.48e-08110
multilaminar epithelium6.15e-0882
extraembryonic membrane6.41e-0814
membranous layer6.41e-0814
squamous epithelium1.28e-0725
organ part1.93e-07219
integument5.42e-0745
integumental system5.42e-0745
somite5.79e-0783
paraxial mesoderm5.79e-0783
presomitic mesoderm5.79e-0783
presumptive segmental plate5.79e-0783
trunk paraxial mesoderm5.79e-0783
presumptive paraxial mesoderm5.79e-0783
embryonic structure8.37e-07605
developing anatomical structure8.37e-07605


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.