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Coexpression cluster:C4585: Difference between revisions

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|ontology_enrichment_disease=DOID:120!3.55e-07!27
|ontology_enrichment_disease=DOID:120!3.55e-07!27
|ontology_enrichment_uberon=UBERON:0007023!5.38e-23!115;UBERON:0001049!5.37e-19!57;UBERON:0005068!5.37e-19!57;UBERON:0006241!5.37e-19!57;UBERON:0007135!5.37e-19!57;UBERON:0000955!2.14e-17!69;UBERON:0006238!2.14e-17!69;UBERON:0002780!4.35e-17!41;UBERON:0001890!4.35e-17!41;UBERON:0006240!4.35e-17!41;UBERON:0003080!2.18e-16!42;UBERON:0002616!4.92e-16!59;UBERON:0001017!6.70e-15!82;UBERON:0000033!6.92e-15!123;UBERON:0000153!1.24e-14!129;UBERON:0007811!1.24e-14!129;UBERON:0002020!4.35e-14!34;UBERON:0003528!4.35e-14!34;UBERON:0005743!5.77e-14!86;UBERON:0001893!8.75e-14!34;UBERON:0001869!3.83e-13!32;UBERON:0002791!5.22e-13!33;UBERON:0003075!1.02e-12!86;UBERON:0007284!1.02e-12!86;UBERON:0002619!3.88e-12!22;UBERON:0002346!1.95e-11!90;UBERON:0000073!4.43e-11!94;UBERON:0001016!4.43e-11!94;UBERON:0001950!1.28e-10!20;UBERON:0000956!6.70e-10!25;UBERON:0000203!6.70e-10!25;UBERON:0004121!4.46e-09!169;UBERON:0004111!5.03e-09!241;UBERON:0003056!5.09e-09!61;UBERON:0000924!2.09e-08!173;UBERON:0006601!2.09e-08!173;UBERON:0000477!5.13e-08!286;UBERON:0000200!2.44e-07!6;UBERON:0003134!7.51e-07!37;UBERON:0000474!7.51e-07!37
|ontology_enrichment_uberon=UBERON:0007023!5.38e-23!115;UBERON:0001049!5.37e-19!57;UBERON:0005068!5.37e-19!57;UBERON:0006241!5.37e-19!57;UBERON:0007135!5.37e-19!57;UBERON:0000955!2.14e-17!69;UBERON:0006238!2.14e-17!69;UBERON:0002780!4.35e-17!41;UBERON:0001890!4.35e-17!41;UBERON:0006240!4.35e-17!41;UBERON:0003080!2.18e-16!42;UBERON:0002616!4.92e-16!59;UBERON:0001017!6.70e-15!82;UBERON:0000033!6.92e-15!123;UBERON:0000153!1.24e-14!129;UBERON:0007811!1.24e-14!129;UBERON:0002020!4.35e-14!34;UBERON:0003528!4.35e-14!34;UBERON:0005743!5.77e-14!86;UBERON:0001893!8.75e-14!34;UBERON:0001869!3.83e-13!32;UBERON:0002791!5.22e-13!33;UBERON:0003075!1.02e-12!86;UBERON:0007284!1.02e-12!86;UBERON:0002619!3.88e-12!22;UBERON:0002346!1.95e-11!90;UBERON:0000073!4.43e-11!94;UBERON:0001016!4.43e-11!94;UBERON:0001950!1.28e-10!20;UBERON:0000956!6.70e-10!25;UBERON:0000203!6.70e-10!25;UBERON:0004121!4.46e-09!169;UBERON:0004111!5.03e-09!241;UBERON:0003056!5.09e-09!61;UBERON:0000924!2.09e-08!173;UBERON:0006601!2.09e-08!173;UBERON:0000477!5.13e-08!286;UBERON:0000200!2.44e-07!6;UBERON:0003134!7.51e-07!37;UBERON:0000474!7.51e-07!37
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090129811061351!HDAC8#55869;3:776.584033613445:2.10837623426304e-09:1.8108281704786e-07!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446124558538827!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157564193947539!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000859252981984718!NFE2#4778;3:77.204260651629:2.17039522930409e-06:7.8433877976917e-05!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00473225800998374!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.00072239418803218!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331011922521256
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}}
}}

Revision as of 14:33, 5 September 2012


Full id: C4585_cerebellum_middle_parietal_occipital_medial_mesothelioma_giant



Phase1 CAGE Peaks

Hg19::chr6:28321811..28321824,-p8@ZNF323
Hg19::chr6:28321827..28321856,-p5@ZNF323
Hg19::chr6:28322004..28322023,-p6@ZNF323


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
mesothelial cell2.60e-0919
squamous epithelial cell8.85e-0762
Uber Anatomy
Ontology termp-valuen
adult organism5.38e-23115
neural tube5.37e-1957
neural rod5.37e-1957
future spinal cord5.37e-1957
neural keel5.37e-1957
brain2.14e-1769
future brain2.14e-1769
regional part of forebrain4.35e-1741
forebrain4.35e-1741
future forebrain4.35e-1741
anterior neural tube2.18e-1642
regional part of brain4.92e-1659
central nervous system6.70e-1582
head6.92e-15123
anterior region of body1.24e-14129
craniocervical region1.24e-14129
gray matter4.35e-1434
brain grey matter4.35e-1434
telencephalon8.75e-1434
cerebral hemisphere3.83e-1332
regional part of telencephalon5.22e-1333
neural plate1.02e-1286
presumptive neural plate1.02e-1286
regional part of cerebral cortex3.88e-1222
neurectoderm1.95e-1190
regional part of nervous system4.43e-1194
nervous system4.43e-1194
neocortex1.28e-1020
cerebral cortex6.70e-1025
pallium6.70e-1025
ectoderm-derived structure4.46e-09169
anatomical conduit5.03e-09241
pre-chordal neural plate5.09e-0961
ectoderm2.09e-08173
presumptive ectoderm2.09e-08173
anatomical cluster5.13e-08286
gyrus2.44e-076
female reproductive organ7.51e-0737
female reproductive system7.51e-0737
Disease
Ontology termp-valuen
female reproductive organ cancer3.55e-0727


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
FOS#235338.99795530889440.001372499272417130.0090129811061351
HDAC8#558693776.5840336134452.10837623426304e-091.8108281704786e-07
JUN#3725312.51282919233630.0005103313992726250.00446124558538827
JUND#372736.994663941871030.002921845042734990.0157564193947539
MAFK#7975327.10073313782995.02195559325033e-050.000859252981984718
NFE2#4778377.2042606516292.17039522930409e-067.8433877976917e-05
NRF1#4899312.21027944771090.0005492172401020010.00473225800998374
TAL1#6886329.86861667744023.75103522793067e-050.00072239418803218
YY1#752834.911170749853860.008441455341808260.0331011922521256



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:C4585&oldid=2133471"