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Coexpression cluster:C689: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0008947!3.14e-17!38;UBERON:0003258!3.14e-17!38;UBERON:0000065!2.91e-16!54;UBERON:0004119!2.43e-14!160;UBERON:0000925!2.43e-14!160;UBERON:0006595!2.43e-14!160;UBERON:0001004!2.33e-13!74;UBERON:0000072!5.08e-12!47;UBERON:0001048!7.24e-12!160;UBERON:0005153!3.38e-11!37;UBERON:0001041!9.69e-11!87;UBERON:0001737!2.53e-10!9;UBERON:0000464!8.50e-10!95;UBERON:0005911!1.96e-09!82;UBERON:0005631!2.77e-09!14;UBERON:0000158!2.77e-09!14;UBERON:0006554!3.82e-09!47;UBERON:0001007!4.94e-09!145;UBERON:0001555!4.94e-09!145;UBERON:0007026!4.94e-09!145;UBERON:0001008!8.85e-09!48;UBERON:0005157!1.63e-08!47;UBERON:0005178!1.79e-08!34;UBERON:0002224!1.79e-08!34;UBERON:0004921!2.26e-08!118;UBERON:0000915!3.17e-08!52;UBERON:0005181!4.79e-08!35;UBERON:0002048!5.89e-08!22;UBERON:0000117!5.89e-08!22;UBERON:0000171!5.89e-08!22;UBERON:0000170!5.89e-08!22;UBERON:0005597!5.89e-08!22;UBERON:0000118!5.89e-08!22;UBERON:0003124!9.00e-08!7;UBERON:0000466!9.09e-08!117;UBERON:0000063!1.58e-07!98;UBERON:0009569!9.24e-07!112
|ontology_enrichment_uberon=UBERON:0008947!3.14e-17!38;UBERON:0003258!3.14e-17!38;UBERON:0000065!2.91e-16!54;UBERON:0004119!2.43e-14!160;UBERON:0000925!2.43e-14!160;UBERON:0006595!2.43e-14!160;UBERON:0001004!2.33e-13!74;UBERON:0000072!5.08e-12!47;UBERON:0001048!7.24e-12!160;UBERON:0005153!3.38e-11!37;UBERON:0001041!9.69e-11!87;UBERON:0001737!2.53e-10!9;UBERON:0000464!8.50e-10!95;UBERON:0005911!1.96e-09!82;UBERON:0005631!2.77e-09!14;UBERON:0000158!2.77e-09!14;UBERON:0006554!3.82e-09!47;UBERON:0001007!4.94e-09!145;UBERON:0001555!4.94e-09!145;UBERON:0007026!4.94e-09!145;UBERON:0001008!8.85e-09!48;UBERON:0005157!1.63e-08!47;UBERON:0005178!1.79e-08!34;UBERON:0002224!1.79e-08!34;UBERON:0004921!2.26e-08!118;UBERON:0000915!3.17e-08!52;UBERON:0005181!4.79e-08!35;UBERON:0002048!5.89e-08!22;UBERON:0000117!5.89e-08!22;UBERON:0000171!5.89e-08!22;UBERON:0000170!5.89e-08!22;UBERON:0005597!5.89e-08!22;UBERON:0000118!5.89e-08!22;UBERON:0003124!9.00e-08!7;UBERON:0000466!9.09e-08!117;UBERON:0000063!1.58e-07!98;UBERON:0009569!9.24e-07!112
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}}
}}

Revision as of 14:24, 26 November 2012


Full id: C689_Alveolar_mesothelioma_Retinal_Mesothelial_Prostate_bile_Tracheal



Phase1 CAGE Peaks

Hg19::chr11:67232723..67232762,-p2@TMEM134
Hg19::chr12:52627019..52627037,+p1@KRT7
Hg19::chr12:52628993..52629014,+p@chr12:52628993..52629014
+
Hg19::chr12:52629037..52629072,+p@chr12:52629037..52629072
+
Hg19::chr12:52629080..52629112,+p@chr12:52629080..52629112
+
Hg19::chr12:52629130..52629159,-p@chr12:52629130..52629159
-
Hg19::chr12:52635300..52635325,+p9@KRT7
Hg19::chr12:52636796..52636807,+p26@KRT7
Hg19::chr12:52636827..52636840,+p3@KRT7
Hg19::chr12:52639223..52639262,+p6@KRT7
Hg19::chr12:52642466..52642508,+p@chr12:52642466..52642508
+
Hg19::chr12:52642530..52642567,+p@chr12:52642530..52642567
+


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
respiratory primordium3.14e-1738
endoderm of foregut3.14e-1738
respiratory tract2.91e-1654
endoderm-derived structure2.43e-14160
endoderm2.43e-14160
presumptive endoderm2.43e-14160
respiratory system2.33e-1374
segment of respiratory tract5.08e-1247
primordium7.24e-12160
epithelial bud3.38e-1137
foregut9.69e-1187
larynx2.53e-109
anatomical space8.50e-1095
endo-epithelium1.96e-0982
extraembryonic membrane2.77e-0914
membranous layer2.77e-0914
urinary system structure3.82e-0947
digestive system4.94e-09145
digestive tract4.94e-09145
primitive gut4.94e-09145
renal system8.85e-0948
epithelial fold1.63e-0847
thoracic cavity element1.79e-0834
thoracic cavity1.79e-0834
subdivision of digestive tract2.26e-08118
thoracic segment of trunk3.17e-0852
thoracic segment organ4.79e-0835
lung5.89e-0822
respiratory tube5.89e-0822
respiration organ5.89e-0822
pair of lungs5.89e-0822
lung primordium5.89e-0822
lung bud5.89e-0822
chorion9.00e-087
immaterial anatomical entity9.09e-08117
organ segment1.58e-0798
subdivision of trunk9.24e-07112
Disease
Ontology termp-valuen
carcinoma1.75e-14106
cell type cancer1.56e-09143


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

No analysis results for this cluster

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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