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Coexpression cluster:C2928: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!2.15e-11!143;DOID:305!1.54e-10!106;DOID:14566!3.09e-10!239;DOID:162!1.76e-09!235
|ontology_enrichment_disease=DOID:0050687!2.15e-11!143;DOID:305!1.54e-10!106;DOID:14566!3.09e-10!239;DOID:162!1.76e-09!235
|ontology_enrichment_uberon=UBERON:0007023!1.53e-22!115;UBERON:0000924!3.02e-20!173;UBERON:0006601!3.02e-20!173;UBERON:0000073!1.10e-19!94;UBERON:0001016!1.10e-19!94;UBERON:0004121!1.01e-18!169;UBERON:0005743!6.81e-18!86;UBERON:0001017!1.82e-17!82;UBERON:0002346!6.34e-16!90;UBERON:0001049!9.24e-16!57;UBERON:0005068!9.24e-16!57;UBERON:0006241!9.24e-16!57;UBERON:0007135!9.24e-16!57;UBERON:0000955!7.13e-15!69;UBERON:0006238!7.13e-15!69;UBERON:0003075!2.40e-14!86;UBERON:0007284!2.40e-14!86;UBERON:0000064!7.18e-14!219;UBERON:0000922!3.71e-13!612;UBERON:0002616!3.72e-13!59;UBERON:0002780!6.60e-13!41;UBERON:0001890!6.60e-13!41;UBERON:0006240!6.60e-13!41;UBERON:0000153!1.09e-12!129;UBERON:0007811!1.09e-12!129;UBERON:0003080!3.75e-12!42;UBERON:0001893!6.54e-12!34;UBERON:0002020!8.04e-12!34;UBERON:0003528!8.04e-12!34;UBERON:0001869!1.06e-11!32;UBERON:0000033!1.11e-11!123;UBERON:0002791!1.62e-11!33;UBERON:0000481!3.31e-11!347;UBERON:0002050!3.38e-11!605;UBERON:0005423!3.38e-11!605;UBERON:0000923!6.83e-11!604;UBERON:0005291!6.83e-11!604;UBERON:0006598!6.83e-11!604;UBERON:0002532!6.83e-11!604;UBERON:0003056!9.59e-10!61;UBERON:0000468!1.34e-09!659;UBERON:0001004!3.52e-09!72;UBERON:0000062!3.81e-09!511;UBERON:0000956!6.10e-09!25;UBERON:0000203!6.10e-09!25;UBERON:0000065!1.49e-08!53;UBERON:0000483!1.80e-08!309;UBERON:0000119!4.39e-08!312;UBERON:0002619!7.52e-08!22;UBERON:0008947!2.46e-07!38;UBERON:0003258!2.46e-07!38;UBERON:0001048!2.46e-07!168;UBERON:0001950!5.12e-07!20;UBERON:0004119!5.28e-07!169;UBERON:0000925!5.28e-07!169;UBERON:0006595!5.28e-07!169
|ontology_enrichment_uberon=UBERON:0007023!1.53e-22!115;UBERON:0000924!3.02e-20!173;UBERON:0006601!3.02e-20!173;UBERON:0000073!1.10e-19!94;UBERON:0001016!1.10e-19!94;UBERON:0004121!1.01e-18!169;UBERON:0005743!6.81e-18!86;UBERON:0001017!1.82e-17!82;UBERON:0002346!6.34e-16!90;UBERON:0001049!9.24e-16!57;UBERON:0005068!9.24e-16!57;UBERON:0006241!9.24e-16!57;UBERON:0007135!9.24e-16!57;UBERON:0000955!7.13e-15!69;UBERON:0006238!7.13e-15!69;UBERON:0003075!2.40e-14!86;UBERON:0007284!2.40e-14!86;UBERON:0000064!7.18e-14!219;UBERON:0000922!3.71e-13!612;UBERON:0002616!3.72e-13!59;UBERON:0002780!6.60e-13!41;UBERON:0001890!6.60e-13!41;UBERON:0006240!6.60e-13!41;UBERON:0000153!1.09e-12!129;UBERON:0007811!1.09e-12!129;UBERON:0003080!3.75e-12!42;UBERON:0001893!6.54e-12!34;UBERON:0002020!8.04e-12!34;UBERON:0003528!8.04e-12!34;UBERON:0001869!1.06e-11!32;UBERON:0000033!1.11e-11!123;UBERON:0002791!1.62e-11!33;UBERON:0000481!3.31e-11!347;UBERON:0002050!3.38e-11!605;UBERON:0005423!3.38e-11!605;UBERON:0000923!6.83e-11!604;UBERON:0005291!6.83e-11!604;UBERON:0006598!6.83e-11!604;UBERON:0002532!6.83e-11!604;UBERON:0003056!9.59e-10!61;UBERON:0000468!1.34e-09!659;UBERON:0001004!3.52e-09!72;UBERON:0000062!3.81e-09!511;UBERON:0000956!6.10e-09!25;UBERON:0000203!6.10e-09!25;UBERON:0000065!1.49e-08!53;UBERON:0000483!1.80e-08!309;UBERON:0000119!4.39e-08!312;UBERON:0002619!7.52e-08!22;UBERON:0008947!2.46e-07!38;UBERON:0003258!2.46e-07!38;UBERON:0001048!2.46e-07!168;UBERON:0001950!5.12e-07!20;UBERON:0004119!5.28e-07!169;UBERON:0000925!5.28e-07!169;UBERON:0006595!5.28e-07!169
|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.00954470586445421
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}}
}}

Revision as of 13:45, 5 September 2012


Full id: C2928_skeletal_neuroepithelioma_neuroectodermal_peripheral_tongue_throat_penis



Phase1 CAGE Peaks

Hg19::chr8:75147731..75147735,-p5@JPH1
Hg19::chr8:75148890..75148893,-p@chr8:75148890..75148893
-
Hg19::chr8:75233646..75233681,-p3@JPH1
Hg19::chr8:75233767..75233785,-p1@JPH1


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 cell1.73e-09254
Uber Anatomy
Ontology termp-valuen
adult organism1.53e-22115
ectoderm3.02e-20173
presumptive ectoderm3.02e-20173
regional part of nervous system1.10e-1994
nervous system1.10e-1994
ectoderm-derived structure1.01e-18169
central nervous system1.82e-1782
neurectoderm6.34e-1690
neural tube9.24e-1657
neural rod9.24e-1657
future spinal cord9.24e-1657
neural keel9.24e-1657
brain7.13e-1569
future brain7.13e-1569
neural plate2.40e-1486
presumptive neural plate2.40e-1486
organ part7.18e-14219
embryo3.71e-13612
regional part of brain3.72e-1359
regional part of forebrain6.60e-1341
forebrain6.60e-1341
future forebrain6.60e-1341
anterior region of body1.09e-12129
craniocervical region1.09e-12129
anterior neural tube3.75e-1242
telencephalon6.54e-1234
gray matter8.04e-1234
brain grey matter8.04e-1234
cerebral hemisphere1.06e-1132
head1.11e-11123
regional part of telencephalon1.62e-1133
multi-tissue structure3.31e-11347
embryonic structure3.38e-11605
developing anatomical structure3.38e-11605
germ layer6.83e-11604
embryonic tissue6.83e-11604
presumptive structure6.83e-11604
epiblast (generic)6.83e-11604
pre-chordal neural plate9.59e-1061
multi-cellular organism1.34e-09659
respiratory system3.52e-0972
organ3.81e-09511
cerebral cortex6.10e-0925
pallium6.10e-0925
respiratory tract1.49e-0853
epithelium1.80e-08309
cell layer4.39e-08312
regional part of cerebral cortex7.52e-0822
respiratory primordium2.46e-0738
endoderm of foregut2.46e-0738
primordium2.46e-07168
neocortex5.12e-0720
endoderm-derived structure5.28e-07169
endoderm5.28e-07169
presumptive endoderm5.28e-07169
Disease
Ontology termp-valuen
cell type cancer2.15e-11143
carcinoma1.54e-10106
disease of cellular proliferation3.09e-10239
cancer1.76e-09235


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)

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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#1488231.35850016966410.001492676882047230.00954470586445421



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.