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Coexpression cluster:C4755: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!4.73e-07!14
|ontology_enrichment_disease=DOID:1749!4.73e-07!14
|ontology_enrichment_uberon=UBERON:0007023!1.04e-32!115;UBERON:0000475!7.25e-23!365;UBERON:0001049!5.92e-22!57;UBERON:0005068!5.92e-22!57;UBERON:0006241!5.92e-22!57;UBERON:0007135!5.92e-22!57;UBERON:0004121!5.66e-21!169;UBERON:0002616!1.42e-20!59;UBERON:0000924!1.70e-19!173;UBERON:0006601!1.70e-19!173;UBERON:0000153!4.24e-19!129;UBERON:0007811!4.24e-19!129;UBERON:0001017!1.54e-18!82;UBERON:0000033!2.45e-18!123;UBERON:0005743!4.58e-18!86;UBERON:0000468!4.94e-18!659;UBERON:0000073!2.58e-17!94;UBERON:0001016!2.58e-17!94;UBERON:0004111!5.03e-17!241;UBERON:0000955!1.52e-16!69;UBERON:0006238!1.52e-16!69;UBERON:0000119!2.18e-16!312;UBERON:0000480!2.85e-16!626;UBERON:0000467!4.27e-16!625;UBERON:0000483!7.82e-16!309;UBERON:0003075!1.28e-15!86;UBERON:0007284!1.28e-15!86;UBERON:0003080!1.89e-15!42;UBERON:0002780!4.61e-15!41;UBERON:0001890!4.61e-15!41;UBERON:0006240!4.61e-15!41;UBERON:0000477!3.20e-14!286;UBERON:0002346!8.13e-14!90;UBERON:0000481!6.83e-13!347;UBERON:0002020!2.10e-12!34;UBERON:0003528!2.10e-12!34;UBERON:0001893!2.95e-12!34;UBERON:0002791!8.13e-12!33;UBERON:0001869!4.02e-11!32;UBERON:0000062!8.66e-11!511;UBERON:0000922!3.12e-10!612;UBERON:0000064!9.08e-10!219;UBERON:0003056!1.16e-09!61;UBERON:0000025!1.62e-09!194;UBERON:0002050!5.62e-09!605;UBERON:0005423!5.62e-09!605;UBERON:0000923!8.50e-09!604;UBERON:0005291!8.50e-09!604;UBERON:0006598!8.50e-09!604;UBERON:0002532!8.50e-09!604;UBERON:0002619!2.41e-08!22;UBERON:0000956!2.49e-08!25;UBERON:0000203!2.49e-08!25;UBERON:0003076!8.37e-08!15;UBERON:0003057!8.37e-08!15;UBERON:0001950!1.85e-07!20;UBERON:0003102!3.31e-07!95;UBERON:0000161!8.65e-07!35
|ontology_enrichment_uberon=UBERON:0007023!1.04e-32!115;UBERON:0000475!7.25e-23!365;UBERON:0001049!5.92e-22!57;UBERON:0005068!5.92e-22!57;UBERON:0006241!5.92e-22!57;UBERON:0007135!5.92e-22!57;UBERON:0004121!5.66e-21!169;UBERON:0002616!1.42e-20!59;UBERON:0000924!1.70e-19!173;UBERON:0006601!1.70e-19!173;UBERON:0000153!4.24e-19!129;UBERON:0007811!4.24e-19!129;UBERON:0001017!1.54e-18!82;UBERON:0000033!2.45e-18!123;UBERON:0005743!4.58e-18!86;UBERON:0000468!4.94e-18!659;UBERON:0000073!2.58e-17!94;UBERON:0001016!2.58e-17!94;UBERON:0004111!5.03e-17!241;UBERON:0000955!1.52e-16!69;UBERON:0006238!1.52e-16!69;UBERON:0000119!2.18e-16!312;UBERON:0000480!2.85e-16!626;UBERON:0000467!4.27e-16!625;UBERON:0000483!7.82e-16!309;UBERON:0003075!1.28e-15!86;UBERON:0007284!1.28e-15!86;UBERON:0003080!1.89e-15!42;UBERON:0002780!4.61e-15!41;UBERON:0001890!4.61e-15!41;UBERON:0006240!4.61e-15!41;UBERON:0000477!3.20e-14!286;UBERON:0002346!8.13e-14!90;UBERON:0000481!6.83e-13!347;UBERON:0002020!2.10e-12!34;UBERON:0003528!2.10e-12!34;UBERON:0001893!2.95e-12!34;UBERON:0002791!8.13e-12!33;UBERON:0001869!4.02e-11!32;UBERON:0000062!8.66e-11!511;UBERON:0000922!3.12e-10!612;UBERON:0000064!9.08e-10!219;UBERON:0003056!1.16e-09!61;UBERON:0000025!1.62e-09!194;UBERON:0002050!5.62e-09!605;UBERON:0005423!5.62e-09!605;UBERON:0000923!8.50e-09!604;UBERON:0005291!8.50e-09!604;UBERON:0006598!8.50e-09!604;UBERON:0002532!8.50e-09!604;UBERON:0002619!2.41e-08!22;UBERON:0000956!2.49e-08!25;UBERON:0000203!2.49e-08!25;UBERON:0003076!8.37e-08!15;UBERON:0003057!8.37e-08!15;UBERON:0001950!1.85e-07!20;UBERON:0003102!3.31e-07!95;UBERON:0000161!8.65e-07!35
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}}
}}

Revision as of 20:18, 8 August 2012


Full id: C4755_heart_oral_salivary_cervical_Mammary_Keratinocyte_skeletal



Phase1 CAGE Peaks

Hg19::chr8:42358653..42358670,-p10@SLC20A2
Hg19::chr8:42358682..42358693,-p8@SLC20A2
Hg19::chr8:42358694..42358706,-p7@SLC20A2


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
endo-epithelial cell4.38e-0843
Uber Anatomy
Ontology termp-valuen
adult organism1.04e-32115
organism subdivision7.25e-23365
neural tube5.92e-2257
neural rod5.92e-2257
future spinal cord5.92e-2257
neural keel5.92e-2257
ectoderm-derived structure5.66e-21169
regional part of brain1.42e-2059
ectoderm1.70e-19173
presumptive ectoderm1.70e-19173
anterior region of body4.24e-19129
craniocervical region4.24e-19129
central nervous system1.54e-1882
head2.45e-18123
multi-cellular organism4.94e-18659
regional part of nervous system2.58e-1794
nervous system2.58e-1794
anatomical conduit5.03e-17241
brain1.52e-1669
future brain1.52e-1669
cell layer2.18e-16312
anatomical group2.85e-16626
anatomical system4.27e-16625
epithelium7.82e-16309
neural plate1.28e-1586
presumptive neural plate1.28e-1586
anterior neural tube1.89e-1542
regional part of forebrain4.61e-1541
forebrain4.61e-1541
future forebrain4.61e-1541
anatomical cluster3.20e-14286
neurectoderm8.13e-1490
multi-tissue structure6.83e-13347
gray matter2.10e-1234
brain grey matter2.10e-1234
telencephalon2.95e-1234
regional part of telencephalon8.13e-1233
cerebral hemisphere4.02e-1132
organ8.66e-11511
embryo3.12e-10612
organ part9.08e-10219
pre-chordal neural plate1.16e-0961
tube1.62e-09194
embryonic structure5.62e-09605
developing anatomical structure5.62e-09605
germ layer8.50e-09604
embryonic tissue8.50e-09604
presumptive structure8.50e-09604
epiblast (generic)8.50e-09604
regional part of cerebral cortex2.41e-0822
cerebral cortex2.49e-0825
pallium2.49e-0825
posterior neural tube8.37e-0815
chordal neural plate8.37e-0815
neocortex1.85e-0720
surface structure3.31e-0795
orifice8.65e-0735
Disease
Ontology termp-valuen
squamous cell carcinoma4.73e-0714


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.