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Coexpression cluster:C3717: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.53e-29!106;DOID:0050687!5.92e-25!143;DOID:162!1.96e-13!235;DOID:14566!9.91e-13!239;DOID:299!5.39e-11!25;DOID:1749!3.53e-09!14
|ontology_enrichment_disease=DOID:305!4.53e-29!106;DOID:0050687!5.92e-25!143;DOID:162!1.96e-13!235;DOID:14566!9.91e-13!239;DOID:299!5.39e-11!25;DOID:1749!3.53e-09!14
|ontology_enrichment_uberon=UBERON:0004119!1.26e-24!169;UBERON:0000925!1.26e-24!169;UBERON:0006595!1.26e-24!169;UBERON:0001007!1.10e-22!155;UBERON:0001555!1.10e-22!155;UBERON:0007026!1.10e-22!155;UBERON:0000077!3.62e-18!130;UBERON:0004921!4.82e-18!129;UBERON:0004185!4.82e-18!129;UBERON:0005911!3.55e-15!82;UBERON:0001041!8.52e-14!98;UBERON:0003104!2.60e-13!238;UBERON:0009142!2.60e-13!238;UBERON:0001004!2.26e-11!72;UBERON:0008947!6.21e-11!38;UBERON:0003258!6.21e-11!38;UBERON:0005177!1.41e-10!107;UBERON:0000065!2.07e-10!53;UBERON:0000481!2.15e-10!347;UBERON:0003929!1.56e-09!54;UBERON:0001737!1.71e-09!9;UBERON:0000466!2.44e-09!126;UBERON:0009569!7.65e-09!113;UBERON:0002100!1.87e-08!216;UBERON:0000072!5.19e-08!46;UBERON:0001048!9.09e-08!168;UBERON:0005153!1.09e-07!37;UBERON:0006554!1.18e-07!44;UBERON:0001008!2.82e-07!45;UBERON:0005172!5.03e-07!55;UBERON:0005173!5.03e-07!55;UBERON:0009497!9.22e-07!25;UBERON:0000015!9.22e-07!25;UBERON:0002423!9.22e-07!25;UBERON:0006235!9.22e-07!25;UBERON:0004161!9.22e-07!25
|ontology_enrichment_uberon=UBERON:0004119!1.26e-24!169;UBERON:0000925!1.26e-24!169;UBERON:0006595!1.26e-24!169;UBERON:0001007!1.10e-22!155;UBERON:0001555!1.10e-22!155;UBERON:0007026!1.10e-22!155;UBERON:0000077!3.62e-18!130;UBERON:0004921!4.82e-18!129;UBERON:0004185!4.82e-18!129;UBERON:0005911!3.55e-15!82;UBERON:0001041!8.52e-14!98;UBERON:0003104!2.60e-13!238;UBERON:0009142!2.60e-13!238;UBERON:0001004!2.26e-11!72;UBERON:0008947!6.21e-11!38;UBERON:0003258!6.21e-11!38;UBERON:0005177!1.41e-10!107;UBERON:0000065!2.07e-10!53;UBERON:0000481!2.15e-10!347;UBERON:0003929!1.56e-09!54;UBERON:0001737!1.71e-09!9;UBERON:0000466!2.44e-09!126;UBERON:0009569!7.65e-09!113;UBERON:0002100!1.87e-08!216;UBERON:0000072!5.19e-08!46;UBERON:0001048!9.09e-08!168;UBERON:0005153!1.09e-07!37;UBERON:0006554!1.18e-07!44;UBERON:0001008!2.82e-07!45;UBERON:0005172!5.03e-07!55;UBERON:0005173!5.03e-07!55;UBERON:0009497!9.22e-07!25;UBERON:0000015!9.22e-07!25;UBERON:0002423!9.22e-07!25;UBERON:0006235!9.22e-07!25;UBERON:0004161!9.22e-07!25
|tf_chipseq_enrich=PRDM1#639;2:87.8873038516405:0.000171624884802908:0.00209152057688809!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.039010823197868!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378119363961817
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}}
}}

Revision as of 12:12, 5 September 2012


Full id: C3717_cervical_bronchogenic_glassy_epitheloid_Hep2_small_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr18:33767302..33767315,-p3@uc002kzp.2
Hg19::chr18:33767331..33767359,-p2@uc002kzp.2
Hg19::chr21:44842602..44842620,-p@chr21:44842602..44842620
-


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 cell9.29e-22254
endodermal cell2.55e-1059
endo-epithelial cell6.52e-0843
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.26e-24169
endoderm1.26e-24169
presumptive endoderm1.26e-24169
digestive system1.10e-22155
digestive tract1.10e-22155
primitive gut1.10e-22155
mixed endoderm/mesoderm-derived structure3.62e-18130
subdivision of digestive tract4.82e-18129
endodermal part of digestive tract4.82e-18129
endo-epithelium3.55e-1582
foregut8.52e-1498
mesenchyme2.60e-13238
entire embryonic mesenchyme2.60e-13238
respiratory system2.26e-1172
respiratory primordium6.21e-1138
endoderm of foregut6.21e-1138
trunk region element1.41e-10107
respiratory tract2.07e-1053
multi-tissue structure2.15e-10347
gut epithelium1.56e-0954
larynx1.71e-099
immaterial anatomical entity2.44e-09126
subdivision of trunk7.65e-09113
trunk1.87e-08216
segment of respiratory tract5.19e-0846
primordium9.09e-08168
epithelial bud1.09e-0737
urinary system structure1.18e-0744
renal system2.82e-0745
abdomen element5.03e-0755
abdominal segment element5.03e-0755
epithelium of foregut-midgut junction9.22e-0725
anatomical boundary9.22e-0725
hepatobiliary system9.22e-0725
foregut-midgut junction9.22e-0725
septum transversum9.22e-0725
Disease
Ontology termp-valuen
carcinoma4.53e-29106
cell type cancer5.92e-25143
cancer1.96e-13235
disease of cellular proliferation9.91e-13239
adenocarcinoma5.39e-1125
squamous cell carcinoma3.53e-0914


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
PRDM1#639287.88730385164050.0001716248848029080.00209152057688809
TFAP2A#7020211.01242291536330.01054990655215560.039010823197868
ZEB1#6935211.25895467836260.01010222676646330.0378119363961817



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3717&oldid=2131030"