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Coexpression cluster:C2768: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.95e-18!106;DOID:0050687!1.43e-11!143
|ontology_enrichment_disease=DOID:305!2.95e-18!106;DOID:0050687!1.43e-11!143
|ontology_enrichment_uberon=UBERON:0007023!1.08e-35!115;UBERON:0000481!6.47e-19!347;UBERON:0004921!6.50e-15!129;UBERON:0004185!6.50e-15!129;UBERON:0004119!6.89e-15!169;UBERON:0000925!6.89e-15!169;UBERON:0006595!6.89e-15!169;UBERON:0001007!1.13e-14!155;UBERON:0001555!1.13e-14!155;UBERON:0007026!1.13e-14!155;UBERON:0001017!1.95e-14!82;UBERON:0001049!2.21e-14!57;UBERON:0005068!2.21e-14!57;UBERON:0006241!2.21e-14!57;UBERON:0007135!2.21e-14!57;UBERON:0003080!7.39e-14!42;UBERON:0005743!1.03e-13!86;UBERON:0002780!2.49e-13!41;UBERON:0001890!2.49e-13!41;UBERON:0006240!2.49e-13!41;UBERON:0000073!1.47e-12!94;UBERON:0001016!1.47e-12!94;UBERON:0000064!1.69e-12!219;UBERON:0000468!5.65e-12!659;UBERON:0003075!7.46e-12!86;UBERON:0007284!7.46e-12!86;UBERON:0002346!9.02e-12!90;UBERON:0000077!9.50e-12!130;UBERON:0000062!9.82e-12!511;UBERON:0002616!1.54e-11!59;UBERON:0000922!1.63e-11!612;UBERON:0000955!6.70e-11!69;UBERON:0006238!6.70e-11!69;UBERON:0001893!1.43e-10!34;UBERON:0002020!1.54e-10!34;UBERON:0003528!1.54e-10!34;UBERON:0002791!2.73e-10!33;UBERON:0002050!4.63e-10!605;UBERON:0005423!4.63e-10!605;UBERON:0000924!4.72e-10!173;UBERON:0006601!4.72e-10!173;UBERON:0004121!5.62e-10!169;UBERON:0000153!5.62e-10!129;UBERON:0007811!5.62e-10!129;UBERON:0000467!7.28e-10!625;UBERON:0001869!9.56e-10!32;UBERON:0000480!9.98e-10!626;UBERON:0000923!1.06e-09!604;UBERON:0005291!1.06e-09!604;UBERON:0006598!1.06e-09!604;UBERON:0002532!1.06e-09!604;UBERON:0001004!1.49e-09!72;UBERON:0000477!2.31e-09!286;UBERON:0003056!2.32e-09!61;UBERON:0000033!4.64e-09!123;UBERON:0000065!6.72e-09!53;UBERON:0000475!7.91e-09!365;UBERON:0001041!8.40e-09!98;UBERON:0002619!1.61e-08!22;UBERON:0001737!3.89e-08!9;UBERON:0001950!6.68e-08!20;UBERON:0000483!1.03e-07!309;UBERON:0008947!1.47e-07!38;UBERON:0003258!1.47e-07!38;UBERON:0003104!1.90e-07!238;UBERON:0009142!1.90e-07!238;UBERON:0004111!1.97e-07!241;UBERON:0000119!2.63e-07!312;UBERON:0000956!2.82e-07!25;UBERON:0000203!2.82e-07!25;UBERON:0001557!5.99e-07!19
|ontology_enrichment_uberon=UBERON:0007023!1.08e-35!115;UBERON:0000481!6.47e-19!347;UBERON:0004921!6.50e-15!129;UBERON:0004185!6.50e-15!129;UBERON:0004119!6.89e-15!169;UBERON:0000925!6.89e-15!169;UBERON:0006595!6.89e-15!169;UBERON:0001007!1.13e-14!155;UBERON:0001555!1.13e-14!155;UBERON:0007026!1.13e-14!155;UBERON:0001017!1.95e-14!82;UBERON:0001049!2.21e-14!57;UBERON:0005068!2.21e-14!57;UBERON:0006241!2.21e-14!57;UBERON:0007135!2.21e-14!57;UBERON:0003080!7.39e-14!42;UBERON:0005743!1.03e-13!86;UBERON:0002780!2.49e-13!41;UBERON:0001890!2.49e-13!41;UBERON:0006240!2.49e-13!41;UBERON:0000073!1.47e-12!94;UBERON:0001016!1.47e-12!94;UBERON:0000064!1.69e-12!219;UBERON:0000468!5.65e-12!659;UBERON:0003075!7.46e-12!86;UBERON:0007284!7.46e-12!86;UBERON:0002346!9.02e-12!90;UBERON:0000077!9.50e-12!130;UBERON:0000062!9.82e-12!511;UBERON:0002616!1.54e-11!59;UBERON:0000922!1.63e-11!612;UBERON:0000955!6.70e-11!69;UBERON:0006238!6.70e-11!69;UBERON:0001893!1.43e-10!34;UBERON:0002020!1.54e-10!34;UBERON:0003528!1.54e-10!34;UBERON:0002791!2.73e-10!33;UBERON:0002050!4.63e-10!605;UBERON:0005423!4.63e-10!605;UBERON:0000924!4.72e-10!173;UBERON:0006601!4.72e-10!173;UBERON:0004121!5.62e-10!169;UBERON:0000153!5.62e-10!129;UBERON:0007811!5.62e-10!129;UBERON:0000467!7.28e-10!625;UBERON:0001869!9.56e-10!32;UBERON:0000480!9.98e-10!626;UBERON:0000923!1.06e-09!604;UBERON:0005291!1.06e-09!604;UBERON:0006598!1.06e-09!604;UBERON:0002532!1.06e-09!604;UBERON:0001004!1.49e-09!72;UBERON:0000477!2.31e-09!286;UBERON:0003056!2.32e-09!61;UBERON:0000033!4.64e-09!123;UBERON:0000065!6.72e-09!53;UBERON:0000475!7.91e-09!365;UBERON:0001041!8.40e-09!98;UBERON:0002619!1.61e-08!22;UBERON:0001737!3.89e-08!9;UBERON:0001950!6.68e-08!20;UBERON:0000483!1.03e-07!309;UBERON:0008947!1.47e-07!38;UBERON:0003258!1.47e-07!38;UBERON:0003104!1.90e-07!238;UBERON:0009142!1.90e-07!238;UBERON:0004111!1.97e-07!241;UBERON:0000119!2.63e-07!312;UBERON:0000956!2.82e-07!25;UBERON:0000203!2.82e-07!25;UBERON:0001557!5.99e-07!19
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}}
}}

Revision as of 14:19, 5 September 2012


Full id: C2768_thyroid_throat_aorta_cervical_small_lung_mesothelioma



Phase1 CAGE Peaks

Hg19::chr4:106816241..106816260,+p4@NPNT
Hg19::chr4:106816592..106816603,+p3@NPNT
Hg19::chr4:106816615..106816642,+p1@NPNT
Hg19::chr4:106816644..106816670,+p2@NPNT


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 cell6.17e-07254
Uber Anatomy
Ontology termp-valuen
adult organism1.08e-35115
multi-tissue structure6.47e-19347
subdivision of digestive tract6.50e-15129
endodermal part of digestive tract6.50e-15129
endoderm-derived structure6.89e-15169
endoderm6.89e-15169
presumptive endoderm6.89e-15169
digestive system1.13e-14155
digestive tract1.13e-14155
primitive gut1.13e-14155
central nervous system1.95e-1482
neural tube2.21e-1457
neural rod2.21e-1457
future spinal cord2.21e-1457
neural keel2.21e-1457
anterior neural tube7.39e-1442
regional part of forebrain2.49e-1341
forebrain2.49e-1341
future forebrain2.49e-1341
regional part of nervous system1.47e-1294
nervous system1.47e-1294
organ part1.69e-12219
multi-cellular organism5.65e-12659
neural plate7.46e-1286
presumptive neural plate7.46e-1286
neurectoderm9.02e-1290
mixed endoderm/mesoderm-derived structure9.50e-12130
organ9.82e-12511
regional part of brain1.54e-1159
embryo1.63e-11612
brain6.70e-1169
future brain6.70e-1169
telencephalon1.43e-1034
gray matter1.54e-1034
brain grey matter1.54e-1034
regional part of telencephalon2.73e-1033
embryonic structure4.63e-10605
developing anatomical structure4.63e-10605
ectoderm4.72e-10173
presumptive ectoderm4.72e-10173
ectoderm-derived structure5.62e-10169
anterior region of body5.62e-10129
craniocervical region5.62e-10129
anatomical system7.28e-10625
cerebral hemisphere9.56e-1032
anatomical group9.98e-10626
germ layer1.06e-09604
embryonic tissue1.06e-09604
presumptive structure1.06e-09604
epiblast (generic)1.06e-09604
respiratory system1.49e-0972
anatomical cluster2.31e-09286
pre-chordal neural plate2.32e-0961
head4.64e-09123
respiratory tract6.72e-0953
organism subdivision7.91e-09365
foregut8.40e-0998
regional part of cerebral cortex1.61e-0822
larynx3.89e-089
neocortex6.68e-0820
epithelium1.03e-07309
respiratory primordium1.47e-0738
endoderm of foregut1.47e-0738
mesenchyme1.90e-07238
entire embryonic mesenchyme1.90e-07238
anatomical conduit1.97e-07241
cell layer2.63e-07312
cerebral cortex2.82e-0725
pallium2.82e-0725
upper respiratory tract5.99e-0719
Disease
Ontology termp-valuen
carcinoma2.95e-18106
cell type cancer1.43e-11143


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
MYC#460945.22228187160940.001344309395272740.00888990875279487
ZEB1#6935312.66632401315790.000793336075912850.00613424346133577



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.