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Coexpression cluster:C4447: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!1.09e-10!143;DOID:305!8.33e-10!106
|ontology_enrichment_disease=DOID:0050687!1.09e-10!143;DOID:305!8.33e-10!106
|ontology_enrichment_uberon=UBERON:0000481!4.14e-22!347;UBERON:0000924!4.28e-20!173;UBERON:0006601!4.28e-20!173;UBERON:0004121!3.09e-19!169;UBERON:0000064!1.89e-17!219;UBERON:0002346!3.48e-17!90;UBERON:0000033!6.82e-17!123;UBERON:0000153!1.13e-16!129;UBERON:0007811!1.13e-16!129;UBERON:0000477!1.19e-16!286;UBERON:0003075!2.29e-16!86;UBERON:0007284!2.29e-16!86;UBERON:0000475!4.36e-15!365;UBERON:0003056!1.01e-14!61;UBERON:0000468!4.11e-14!659;UBERON:0000922!4.43e-14!612;UBERON:0005743!1.81e-13!86;UBERON:0000119!1.89e-13!312;UBERON:0000483!2.85e-13!309;UBERON:0000073!4.32e-13!94;UBERON:0001016!4.32e-13!94;UBERON:0002050!2.04e-12!605;UBERON:0005423!2.04e-12!605;UBERON:0001017!3.62e-12!82;UBERON:0000923!4.53e-12!604;UBERON:0005291!4.53e-12!604;UBERON:0006598!4.53e-12!604;UBERON:0002532!4.53e-12!604;UBERON:0000955!9.65e-12!69;UBERON:0006238!9.65e-12!69;UBERON:0000467!2.82e-11!625;UBERON:0000480!3.22e-11!626;UBERON:0002616!3.44e-11!59;UBERON:0007023!4.72e-11!115;UBERON:0001950!5.51e-11!20;UBERON:0000062!1.68e-10!511;UBERON:0001869!4.57e-10!32;UBERON:0003080!4.88e-10!42;UBERON:0004111!5.00e-10!241;UBERON:0002619!5.73e-10!22;UBERON:0002780!7.28e-10!41;UBERON:0001890!7.28e-10!41;UBERON:0006240!7.28e-10!41;UBERON:0001893!1.58e-09!34;UBERON:0001049!2.42e-09!57;UBERON:0005068!2.42e-09!57;UBERON:0006241!2.42e-09!57;UBERON:0007135!2.42e-09!57;UBERON:0002791!5.08e-09!33;UBERON:0002020!6.63e-09!34;UBERON:0003528!6.63e-09!34;UBERON:0000956!1.71e-08!25;UBERON:0000203!1.71e-08!25;UBERON:0002113!3.78e-08!27;UBERON:0003918!3.78e-08!27;UBERON:0005095!3.78e-08!27;UBERON:0007687!3.78e-08!27;UBERON:0000489!4.11e-08!32;UBERON:0003103!1.31e-07!69;UBERON:0001444!1.49e-07!48;UBERON:0005177!1.85e-07!107;UBERON:0000025!4.29e-07!194;UBERON:0000020!4.83e-07!23
|ontology_enrichment_uberon=UBERON:0000481!4.14e-22!347;UBERON:0000924!4.28e-20!173;UBERON:0006601!4.28e-20!173;UBERON:0004121!3.09e-19!169;UBERON:0000064!1.89e-17!219;UBERON:0002346!3.48e-17!90;UBERON:0000033!6.82e-17!123;UBERON:0000153!1.13e-16!129;UBERON:0007811!1.13e-16!129;UBERON:0000477!1.19e-16!286;UBERON:0003075!2.29e-16!86;UBERON:0007284!2.29e-16!86;UBERON:0000475!4.36e-15!365;UBERON:0003056!1.01e-14!61;UBERON:0000468!4.11e-14!659;UBERON:0000922!4.43e-14!612;UBERON:0005743!1.81e-13!86;UBERON:0000119!1.89e-13!312;UBERON:0000483!2.85e-13!309;UBERON:0000073!4.32e-13!94;UBERON:0001016!4.32e-13!94;UBERON:0002050!2.04e-12!605;UBERON:0005423!2.04e-12!605;UBERON:0001017!3.62e-12!82;UBERON:0000923!4.53e-12!604;UBERON:0005291!4.53e-12!604;UBERON:0006598!4.53e-12!604;UBERON:0002532!4.53e-12!604;UBERON:0000955!9.65e-12!69;UBERON:0006238!9.65e-12!69;UBERON:0000467!2.82e-11!625;UBERON:0000480!3.22e-11!626;UBERON:0002616!3.44e-11!59;UBERON:0007023!4.72e-11!115;UBERON:0001950!5.51e-11!20;UBERON:0000062!1.68e-10!511;UBERON:0001869!4.57e-10!32;UBERON:0003080!4.88e-10!42;UBERON:0004111!5.00e-10!241;UBERON:0002619!5.73e-10!22;UBERON:0002780!7.28e-10!41;UBERON:0001890!7.28e-10!41;UBERON:0006240!7.28e-10!41;UBERON:0001893!1.58e-09!34;UBERON:0001049!2.42e-09!57;UBERON:0005068!2.42e-09!57;UBERON:0006241!2.42e-09!57;UBERON:0007135!2.42e-09!57;UBERON:0002791!5.08e-09!33;UBERON:0002020!6.63e-09!34;UBERON:0003528!6.63e-09!34;UBERON:0000956!1.71e-08!25;UBERON:0000203!1.71e-08!25;UBERON:0002113!3.78e-08!27;UBERON:0003918!3.78e-08!27;UBERON:0005095!3.78e-08!27;UBERON:0007687!3.78e-08!27;UBERON:0000489!4.11e-08!32;UBERON:0003103!1.31e-07!69;UBERON:0001444!1.49e-07!48;UBERON:0005177!1.85e-07!107;UBERON:0000025!4.29e-07!194;UBERON:0000020!4.83e-07!23
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}}
}}

Revision as of 20:02, 8 August 2012


Full id: C4447_mesothelioma_Wilms_leiomyoblastoma_large_endometrial_serous_merkel



Phase1 CAGE Peaks

Hg19::chr5:107007726..107007737,-p@chr5:107007726..107007737
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Hg19::chr5:107007827..107007856,-p@chr5:107007827..107007856
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Hg19::chr5:107007859..107007895,-p@chr5:107007859..107007895
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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 cell6.14e-14254
Uber Anatomy
Ontology termp-valuen
multi-tissue structure4.14e-22347
ectoderm4.28e-20173
presumptive ectoderm4.28e-20173
ectoderm-derived structure3.09e-19169
organ part1.89e-17219
neurectoderm3.48e-1790
head6.82e-17123
anterior region of body1.13e-16129
craniocervical region1.13e-16129
anatomical cluster1.19e-16286
neural plate2.29e-1686
presumptive neural plate2.29e-1686
organism subdivision4.36e-15365
pre-chordal neural plate1.01e-1461
multi-cellular organism4.11e-14659
embryo4.43e-14612
cell layer1.89e-13312
epithelium2.85e-13309
regional part of nervous system4.32e-1394
nervous system4.32e-1394
embryonic structure2.04e-12605
developing anatomical structure2.04e-12605
central nervous system3.62e-1282
germ layer4.53e-12604
embryonic tissue4.53e-12604
presumptive structure4.53e-12604
epiblast (generic)4.53e-12604
brain9.65e-1269
future brain9.65e-1269
anatomical system2.82e-11625
anatomical group3.22e-11626
regional part of brain3.44e-1159
adult organism4.72e-11115
neocortex5.51e-1120
organ1.68e-10511
cerebral hemisphere4.57e-1032
anterior neural tube4.88e-1042
anatomical conduit5.00e-10241
regional part of cerebral cortex5.73e-1022
regional part of forebrain7.28e-1041
forebrain7.28e-1041
future forebrain7.28e-1041
telencephalon1.58e-0934
neural tube2.42e-0957
neural rod2.42e-0957
future spinal cord2.42e-0957
neural keel2.42e-0957
regional part of telencephalon5.08e-0933
gray matter6.63e-0934
brain grey matter6.63e-0934
cerebral cortex1.71e-0825
pallium1.71e-0825
kidney3.78e-0827
kidney mesenchyme3.78e-0827
kidney rudiment3.78e-0827
kidney field3.78e-0827
cavitated compound organ4.11e-0832
compound organ1.31e-0769
subdivision of head1.49e-0748
trunk region element1.85e-07107
tube4.29e-07194
sense organ4.83e-0723
Disease
Ontology termp-valuen
cell type cancer1.09e-10143
carcinoma8.33e-10106


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


No analysis results for this cluster

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.