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Coexpression cluster:C4585: Difference between revisions

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|full_id=C4585_cerebellum_middle_parietal_occipital_medial_mesothelioma_giant
|full_id=C4585_cerebellum_middle_parietal_occipital_medial_mesothelioma_giant
|id=C4585
|id=C4585
|ontology_enrichment_celltype=CL:0000077!2.60e-09!19;CL:0000076!8.85e-07!62
|ontology_enrichment_celltype=CL:0000077!1.16e-10!19
|ontology_enrichment_disease=DOID:120!3.55e-07!27
|ontology_enrichment_disease=
|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:0000073!7.42e-23!53;UBERON:0002616!7.42e-23!53;UBERON:0001049!5.24e-21!56;UBERON:0005068!5.24e-21!56;UBERON:0006241!5.24e-21!56;UBERON:0007135!5.24e-21!56;UBERON:0000955!1.28e-19!68;UBERON:0006238!1.28e-19!68;UBERON:0007023!5.11e-19!114;UBERON:0002780!2.59e-18!41;UBERON:0001890!2.59e-18!41;UBERON:0003080!2.59e-18!41;UBERON:0006240!2.59e-18!41;UBERON:0003528!6.88e-16!34;UBERON:0002020!6.88e-16!34;UBERON:0001017!1.45e-15!81;UBERON:0001869!1.27e-14!32;UBERON:0001893!1.31e-14!34;UBERON:0002791!3.34e-14!32;UBERON:0002619!1.29e-13!22;UBERON:0001950!2.44e-13!20;UBERON:0001016!8.05e-13!89;UBERON:0003075!1.15e-11!82;UBERON:0007284!1.15e-11!82;UBERON:0000956!1.99e-11!25;UBERON:0000203!1.99e-11!25;UBERON:0010371!5.83e-11!104;UBERON:0002346!1.23e-10!86;UBERON:0010314!1.94e-10!132;UBERON:0000200!1.22e-09!6;UBERON:0003056!1.44e-09!61;UBERON:0011216!1.35e-08!223;UBERON:0004121!1.52e-07!171;UBERON:0000924!1.52e-07!171;UBERON:0006601!1.52e-07!171
|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
|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 16:04, 19 October 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><br>


Cell Type
Ontology termp-valuen
mesothelial cell1.16e-1019
Uber Anatomy
Ontology termp-valuen
regional part of nervous system7.42e-2353
regional part of brain7.42e-2353
neural tube5.24e-2156
neural rod5.24e-2156
future spinal cord5.24e-2156
neural keel5.24e-2156
brain1.28e-1968
future brain1.28e-1968
adult organism5.11e-19114
regional part of forebrain2.59e-1841
forebrain2.59e-1841
anterior neural tube2.59e-1841
future forebrain2.59e-1841
brain grey matter6.88e-1634
gray matter6.88e-1634
central nervous system1.45e-1581
cerebral hemisphere1.27e-1432
telencephalon1.31e-1434
regional part of telencephalon3.34e-1432
regional part of cerebral cortex1.29e-1322
neocortex2.44e-1320
nervous system8.05e-1389
neural plate1.15e-1182
presumptive neural plate1.15e-1182
cerebral cortex1.99e-1125
pallium1.99e-1125
ecto-epithelium5.83e-11104
neurectoderm1.23e-1086
structure with developmental contribution from neural crest1.94e-10132
gyrus1.22e-096
pre-chordal neural plate1.44e-0961
organ system subdivision1.35e-08223
ectoderm-derived structure1.52e-07171
ectoderm1.52e-07171
presumptive ectoderm1.52e-07171


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.