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Coexpression cluster:C1683: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!2.64e-11!143;DOID:305!4.82e-10!106;DOID:162!5.05e-07!235
|ontology_enrichment_disease=DOID:0050687!2.64e-11!143;DOID:305!4.82e-10!106;DOID:162!5.05e-07!235
|ontology_enrichment_uberon=UBERON:0002780!4.42e-17!41;UBERON:0001890!4.42e-17!41;UBERON:0006240!4.42e-17!41;UBERON:0001049!5.81e-17!57;UBERON:0005068!5.81e-17!57;UBERON:0006241!5.81e-17!57;UBERON:0007135!5.81e-17!57;UBERON:0003080!2.96e-16!42;UBERON:0001017!7.77e-16!82;UBERON:0004121!8.81e-16!169;UBERON:0000924!1.95e-15!173;UBERON:0006601!1.95e-15!173;UBERON:0002020!3.28e-15!34;UBERON:0003528!3.28e-15!34;UBERON:0005743!4.13e-15!86;UBERON:0003075!4.39e-15!86;UBERON:0007284!4.39e-15!86;UBERON:0001893!9.49e-15!34;UBERON:0001869!1.01e-14!32;UBERON:0002791!1.83e-14!33;UBERON:0007023!1.86e-14!115;UBERON:0002346!1.97e-14!90;UBERON:0002616!2.62e-14!59;UBERON:0000955!6.66e-14!69;UBERON:0006238!6.66e-14!69;UBERON:0003056!8.14e-14!61;UBERON:0000073!1.48e-13!94;UBERON:0001016!1.48e-13!94;UBERON:0000153!1.23e-12!129;UBERON:0007811!1.23e-12!129;UBERON:0000033!1.55e-12!123;UBERON:0000956!2.86e-11!25;UBERON:0000203!2.86e-11!25;UBERON:0002619!3.42e-10!22;UBERON:0001950!3.80e-09!20;UBERON:0000064!5.88e-08!219
|ontology_enrichment_uberon=UBERON:0002780!4.42e-17!41;UBERON:0001890!4.42e-17!41;UBERON:0006240!4.42e-17!41;UBERON:0001049!5.81e-17!57;UBERON:0005068!5.81e-17!57;UBERON:0006241!5.81e-17!57;UBERON:0007135!5.81e-17!57;UBERON:0003080!2.96e-16!42;UBERON:0001017!7.77e-16!82;UBERON:0004121!8.81e-16!169;UBERON:0000924!1.95e-15!173;UBERON:0006601!1.95e-15!173;UBERON:0002020!3.28e-15!34;UBERON:0003528!3.28e-15!34;UBERON:0005743!4.13e-15!86;UBERON:0003075!4.39e-15!86;UBERON:0007284!4.39e-15!86;UBERON:0001893!9.49e-15!34;UBERON:0001869!1.01e-14!32;UBERON:0002791!1.83e-14!33;UBERON:0007023!1.86e-14!115;UBERON:0002346!1.97e-14!90;UBERON:0002616!2.62e-14!59;UBERON:0000955!6.66e-14!69;UBERON:0006238!6.66e-14!69;UBERON:0003056!8.14e-14!61;UBERON:0000073!1.48e-13!94;UBERON:0001016!1.48e-13!94;UBERON:0000153!1.23e-12!129;UBERON:0007811!1.23e-12!129;UBERON:0000033!1.55e-12!123;UBERON:0000956!2.86e-11!25;UBERON:0000203!2.86e-11!25;UBERON:0002619!3.42e-10!22;UBERON:0001950!3.80e-09!20;UBERON:0000064!5.88e-08!219
|tf_chipseq_enrich=CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138470339839381
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}}
}}

Revision as of 14:16, 5 September 2012


Full id: C1683_pancreatic_somatostatinoma_temporal_mesothelioma_occipital_seminal_parietal



Phase1 CAGE Peaks

Hg19::chr12:67101278..67101284,-p@chr12:67101278..67101284
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Hg19::chr12:67208365..67208370,-p@chr12:67208365..67208370
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Hg19::chr12:67372998..67373003,-p@chr12:67372998..67373003
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Hg19::chr12:67463617..67463639,-p@chr12:67463617..67463639
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Hg19::chr12:67463640..67463668,-p@chr12:67463640..67463668
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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 cell4.27e-08254
Uber Anatomy
Ontology termp-valuen
regional part of forebrain4.42e-1741
forebrain4.42e-1741
future forebrain4.42e-1741
neural tube5.81e-1757
neural rod5.81e-1757
future spinal cord5.81e-1757
neural keel5.81e-1757
anterior neural tube2.96e-1642
central nervous system7.77e-1682
ectoderm-derived structure8.81e-16169
ectoderm1.95e-15173
presumptive ectoderm1.95e-15173
gray matter3.28e-1534
brain grey matter3.28e-1534
neural plate4.39e-1586
presumptive neural plate4.39e-1586
telencephalon9.49e-1534
cerebral hemisphere1.01e-1432
regional part of telencephalon1.83e-1433
adult organism1.86e-14115
neurectoderm1.97e-1490
regional part of brain2.62e-1459
brain6.66e-1469
future brain6.66e-1469
pre-chordal neural plate8.14e-1461
regional part of nervous system1.48e-1394
nervous system1.48e-1394
anterior region of body1.23e-12129
craniocervical region1.23e-12129
head1.55e-12123
cerebral cortex2.86e-1125
pallium2.86e-1125
regional part of cerebral cortex3.42e-1022
neocortex3.80e-0920
organ part5.88e-08219
Disease
Ontology termp-valuen
cell type cancer2.64e-11143
carcinoma4.82e-10106
cancer5.05e-07235


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
CTBP2#1488225.08680013573130.002461438599678380.0138470339839381



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.