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Coexpression cluster:C2538: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.53e-30!115;UBERON:0001017!3.00e-28!82;UBERON:0005743!1.75e-27!86;UBERON:0000073!9.14e-27!94;UBERON:0001016!9.14e-27!94;UBERON:0000955!6.50e-25!69;UBERON:0006238!6.50e-25!69;UBERON:0001049!8.96e-24!57;UBERON:0005068!8.96e-24!57;UBERON:0006241!8.96e-24!57;UBERON:0007135!8.96e-24!57;UBERON:0002616!1.87e-23!59;UBERON:0003080!1.32e-20!42;UBERON:0002346!1.39e-20!90;UBERON:0002780!2.13e-20!41;UBERON:0001890!2.13e-20!41;UBERON:0006240!2.13e-20!41;UBERON:0000924!3.48e-20!173;UBERON:0006601!3.48e-20!173;UBERON:0003075!3.66e-19!86;UBERON:0007284!3.66e-19!86;UBERON:0004121!6.90e-19!169;UBERON:0000153!8.18e-18!129;UBERON:0007811!8.18e-18!129;UBERON:0000033!1.06e-17!123;UBERON:0001893!1.22e-17!34;UBERON:0002020!2.34e-17!34;UBERON:0003528!2.34e-17!34;UBERON:0002791!2.93e-17!33;UBERON:0001869!1.33e-16!32;UBERON:0003056!4.83e-15!61;UBERON:0000956!4.99e-14!25;UBERON:0000203!4.99e-14!25;UBERON:0000475!6.82e-14!365;UBERON:0000481!9.26e-13!347;UBERON:0002619!1.58e-12!22;UBERON:0000062!2.59e-12!511;UBERON:0001950!1.77e-11!20;UBERON:0000468!1.87e-11!659;UBERON:0000477!2.92e-11!286;UBERON:0004111!7.08e-10!241;UBERON:0000064!1.96e-09!219;UBERON:0000483!4.17e-08!309;UBERON:0000480!4.56e-08!626;UBERON:0000119!6.66e-08!312;UBERON:0000467!7.00e-08!625;UBERON:0000025!7.63e-08!194;UBERON:0000922!9.33e-08!612
|ontology_enrichment_uberon=UBERON:0007023!2.53e-30!115;UBERON:0001017!3.00e-28!82;UBERON:0005743!1.75e-27!86;UBERON:0000073!9.14e-27!94;UBERON:0001016!9.14e-27!94;UBERON:0000955!6.50e-25!69;UBERON:0006238!6.50e-25!69;UBERON:0001049!8.96e-24!57;UBERON:0005068!8.96e-24!57;UBERON:0006241!8.96e-24!57;UBERON:0007135!8.96e-24!57;UBERON:0002616!1.87e-23!59;UBERON:0003080!1.32e-20!42;UBERON:0002346!1.39e-20!90;UBERON:0002780!2.13e-20!41;UBERON:0001890!2.13e-20!41;UBERON:0006240!2.13e-20!41;UBERON:0000924!3.48e-20!173;UBERON:0006601!3.48e-20!173;UBERON:0003075!3.66e-19!86;UBERON:0007284!3.66e-19!86;UBERON:0004121!6.90e-19!169;UBERON:0000153!8.18e-18!129;UBERON:0007811!8.18e-18!129;UBERON:0000033!1.06e-17!123;UBERON:0001893!1.22e-17!34;UBERON:0002020!2.34e-17!34;UBERON:0003528!2.34e-17!34;UBERON:0002791!2.93e-17!33;UBERON:0001869!1.33e-16!32;UBERON:0003056!4.83e-15!61;UBERON:0000956!4.99e-14!25;UBERON:0000203!4.99e-14!25;UBERON:0000475!6.82e-14!365;UBERON:0000481!9.26e-13!347;UBERON:0002619!1.58e-12!22;UBERON:0000062!2.59e-12!511;UBERON:0001950!1.77e-11!20;UBERON:0000468!1.87e-11!659;UBERON:0000477!2.92e-11!286;UBERON:0004111!7.08e-10!241;UBERON:0000064!1.96e-09!219;UBERON:0000483!4.17e-08!309;UBERON:0000480!4.56e-08!626;UBERON:0000119!6.66e-08!312;UBERON:0000467!7.00e-08!625;UBERON:0000025!7.63e-08!194;UBERON:0000922!9.33e-08!612
|tf_chipseq_enrich=GATA3#2625;2:13.618258178603:0.0076966520809334:0.0316942925116554
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}}
}}

Revision as of 12:00, 5 September 2012


Full id: C2538_parietal_occipital_uterus_cervix_rectum_brain_duodenum



Phase1 CAGE Peaks

Hg19::chr1:164557736..164557744,+p@chr1:164557736..164557744
+
Hg19::chr1:164568324..164568328,+p@chr1:164568324..164568328
+
Hg19::chr1:164600535..164600539,+p@chr1:164600535..164600539
+
Hg19::chr1:164693945..164693950,+p@chr1:164693945..164693950
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.53e-30115
central nervous system3.00e-2882
regional part of nervous system9.14e-2794
nervous system9.14e-2794
brain6.50e-2569
future brain6.50e-2569
neural tube8.96e-2457
neural rod8.96e-2457
future spinal cord8.96e-2457
neural keel8.96e-2457
regional part of brain1.87e-2359
anterior neural tube1.32e-2042
neurectoderm1.39e-2090
regional part of forebrain2.13e-2041
forebrain2.13e-2041
future forebrain2.13e-2041
ectoderm3.48e-20173
presumptive ectoderm3.48e-20173
neural plate3.66e-1986
presumptive neural plate3.66e-1986
ectoderm-derived structure6.90e-19169
anterior region of body8.18e-18129
craniocervical region8.18e-18129
head1.06e-17123
telencephalon1.22e-1734
gray matter2.34e-1734
brain grey matter2.34e-1734
regional part of telencephalon2.93e-1733
cerebral hemisphere1.33e-1632
pre-chordal neural plate4.83e-1561
cerebral cortex4.99e-1425
pallium4.99e-1425
organism subdivision6.82e-14365
multi-tissue structure9.26e-13347
regional part of cerebral cortex1.58e-1222
organ2.59e-12511
neocortex1.77e-1120
multi-cellular organism1.87e-11659
anatomical cluster2.92e-11286
anatomical conduit7.08e-10241
organ part1.96e-09219
epithelium4.17e-08309
anatomical group4.56e-08626
cell layer6.66e-08312
anatomical system7.00e-08625
tube7.63e-08194
embryo9.33e-08612


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
GATA3#2625213.6182581786030.00769665208093340.0316942925116554



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.

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