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Coexpression cluster:C3171: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!3.28e-07!14
|ontology_enrichment_disease=DOID:2394!3.28e-07!14
|ontology_enrichment_uberon=UBERON:0005743!3.49e-26!86;UBERON:0001049!1.54e-24!57;UBERON:0005068!1.54e-24!57;UBERON:0006241!1.54e-24!57;UBERON:0007135!1.54e-24!57;UBERON:0000073!6.70e-24!94;UBERON:0001016!6.70e-24!94;UBERON:0000955!9.02e-24!69;UBERON:0006238!9.02e-24!69;UBERON:0001017!1.87e-23!82;UBERON:0002616!4.09e-23!59;UBERON:0003075!8.08e-21!86;UBERON:0007284!8.08e-21!86;UBERON:0000025!9.71e-21!194;UBERON:0002346!1.17e-19!90;UBERON:0002020!5.66e-17!34;UBERON:0003528!5.66e-17!34;UBERON:0001893!9.09e-17!34;UBERON:0007023!2.38e-16!115;UBERON:0002791!3.31e-16!33;UBERON:0002780!4.37e-16!41;UBERON:0001890!4.37e-16!41;UBERON:0006240!4.37e-16!41;UBERON:0000119!2.02e-15!312;UBERON:0003080!2.22e-15!42;UBERON:0001869!4.06e-15!32;UBERON:0000483!1.29e-14!309;UBERON:0004111!6.10e-14!241;UBERON:0003056!7.34e-14!61;UBERON:0000481!1.74e-12!347;UBERON:0002619!7.18e-12!22;UBERON:0000033!1.47e-11!123;UBERON:0000477!3.10e-11!286;UBERON:0000153!6.52e-11!129;UBERON:0007811!6.52e-11!129;UBERON:0003076!7.16e-11!15;UBERON:0003057!7.16e-11!15;UBERON:0001950!1.65e-10!20;UBERON:0000956!1.76e-10!25;UBERON:0000203!1.76e-10!25;UBERON:0005172!1.06e-09!55;UBERON:0005173!1.06e-09!55;UBERON:0004732!2.79e-09!13;UBERON:0000475!6.38e-09!365;UBERON:0002308!1.48e-08!9;UBERON:0000125!1.48e-08!9;UBERON:0009497!1.87e-08!25;UBERON:0000015!1.87e-08!25;UBERON:0002423!1.87e-08!25;UBERON:0006235!1.87e-08!25;UBERON:0004161!1.87e-08!25;UBERON:0004733!2.18e-08!12;UBERON:0002028!2.18e-08!12;UBERON:0007277!2.18e-08!12;UBERON:0009854!2.35e-08!23;UBERON:0000466!3.19e-08!126;UBERON:0002420!3.74e-08!9;UBERON:0007245!3.74e-08!9;UBERON:0010009!3.74e-08!9;UBERON:0010011!3.74e-08!9;UBERON:0000454!3.74e-08!9;UBERON:0008835!5.05e-08!22;UBERON:0003894!5.05e-08!22;UBERON:0005177!7.52e-08!107;UBERON:0004121!9.45e-08!169;UBERON:0009856!9.88e-08!26;UBERON:0002417!1.41e-07!61;UBERON:0000916!1.41e-07!61;UBERON:0000924!1.84e-07!173;UBERON:0006601!1.84e-07!173;UBERON:0007499!2.09e-07!25;UBERON:0000064!4.12e-07!219;UBERON:0009663!7.29e-07!7
|ontology_enrichment_uberon=UBERON:0005743!3.49e-26!86;UBERON:0001049!1.54e-24!57;UBERON:0005068!1.54e-24!57;UBERON:0006241!1.54e-24!57;UBERON:0007135!1.54e-24!57;UBERON:0000073!6.70e-24!94;UBERON:0001016!6.70e-24!94;UBERON:0000955!9.02e-24!69;UBERON:0006238!9.02e-24!69;UBERON:0001017!1.87e-23!82;UBERON:0002616!4.09e-23!59;UBERON:0003075!8.08e-21!86;UBERON:0007284!8.08e-21!86;UBERON:0000025!9.71e-21!194;UBERON:0002346!1.17e-19!90;UBERON:0002020!5.66e-17!34;UBERON:0003528!5.66e-17!34;UBERON:0001893!9.09e-17!34;UBERON:0007023!2.38e-16!115;UBERON:0002791!3.31e-16!33;UBERON:0002780!4.37e-16!41;UBERON:0001890!4.37e-16!41;UBERON:0006240!4.37e-16!41;UBERON:0000119!2.02e-15!312;UBERON:0003080!2.22e-15!42;UBERON:0001869!4.06e-15!32;UBERON:0000483!1.29e-14!309;UBERON:0004111!6.10e-14!241;UBERON:0003056!7.34e-14!61;UBERON:0000481!1.74e-12!347;UBERON:0002619!7.18e-12!22;UBERON:0000033!1.47e-11!123;UBERON:0000477!3.10e-11!286;UBERON:0000153!6.52e-11!129;UBERON:0007811!6.52e-11!129;UBERON:0003076!7.16e-11!15;UBERON:0003057!7.16e-11!15;UBERON:0001950!1.65e-10!20;UBERON:0000956!1.76e-10!25;UBERON:0000203!1.76e-10!25;UBERON:0005172!1.06e-09!55;UBERON:0005173!1.06e-09!55;UBERON:0004732!2.79e-09!13;UBERON:0000475!6.38e-09!365;UBERON:0002308!1.48e-08!9;UBERON:0000125!1.48e-08!9;UBERON:0009497!1.87e-08!25;UBERON:0000015!1.87e-08!25;UBERON:0002423!1.87e-08!25;UBERON:0006235!1.87e-08!25;UBERON:0004161!1.87e-08!25;UBERON:0004733!2.18e-08!12;UBERON:0002028!2.18e-08!12;UBERON:0007277!2.18e-08!12;UBERON:0009854!2.35e-08!23;UBERON:0000466!3.19e-08!126;UBERON:0002420!3.74e-08!9;UBERON:0007245!3.74e-08!9;UBERON:0010009!3.74e-08!9;UBERON:0010011!3.74e-08!9;UBERON:0000454!3.74e-08!9;UBERON:0008835!5.05e-08!22;UBERON:0003894!5.05e-08!22;UBERON:0005177!7.52e-08!107;UBERON:0004121!9.45e-08!169;UBERON:0009856!9.88e-08!26;UBERON:0002417!1.41e-07!61;UBERON:0000916!1.41e-07!61;UBERON:0000924!1.84e-07!173;UBERON:0006601!1.84e-07!173;UBERON:0007499!2.09e-07!25;UBERON:0000064!4.12e-07!219;UBERON:0009663!7.29e-07!7
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}}
}}

Revision as of 18:57, 8 August 2012


Full id: C3171_optic_thalamus_Mesothelial_diencephalon_Retinal_spinal_occipital



Phase1 CAGE Peaks

Hg19::chr11:61536730..61536771,+p@chr11:61536730..61536771
+
Hg19::chr11:61537818..61537845,+p@chr11:61537818..61537845
+
Hg19::chr11:61538994..61539023,+p@chr11:61538994..61539023
+


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
mesothelial cell1.09e-0919
Uber Anatomy
Ontology termp-valuen
neural tube1.54e-2457
neural rod1.54e-2457
future spinal cord1.54e-2457
neural keel1.54e-2457
regional part of nervous system6.70e-2494
nervous system6.70e-2494
brain9.02e-2469
future brain9.02e-2469
central nervous system1.87e-2382
regional part of brain4.09e-2359
neural plate8.08e-2186
presumptive neural plate8.08e-2186
tube9.71e-21194
neurectoderm1.17e-1990
gray matter5.66e-1734
brain grey matter5.66e-1734
telencephalon9.09e-1734
adult organism2.38e-16115
regional part of telencephalon3.31e-1633
regional part of forebrain4.37e-1641
forebrain4.37e-1641
future forebrain4.37e-1641
cell layer2.02e-15312
anterior neural tube2.22e-1542
cerebral hemisphere4.06e-1532
epithelium1.29e-14309
anatomical conduit6.10e-14241
pre-chordal neural plate7.34e-1461
multi-tissue structure1.74e-12347
regional part of cerebral cortex7.18e-1222
head1.47e-11123
anatomical cluster3.10e-11286
anterior region of body6.52e-11129
craniocervical region6.52e-11129
posterior neural tube7.16e-1115
chordal neural plate7.16e-1115
neocortex1.65e-1020
cerebral cortex1.76e-1025
pallium1.76e-1025
abdomen element1.06e-0955
abdominal segment element1.06e-0955
segmental subdivision of nervous system2.79e-0913
organism subdivision6.38e-09365
nucleus of brain1.48e-089
neural nucleus1.48e-089
epithelium of foregut-midgut junction1.87e-0825
anatomical boundary1.87e-0825
hepatobiliary system1.87e-0825
foregut-midgut junction1.87e-0825
septum transversum1.87e-0825
segmental subdivision of hindbrain2.18e-0812
hindbrain2.18e-0812
presumptive hindbrain2.18e-0812
digestive tract diverticulum2.35e-0823
immaterial anatomical entity3.19e-08126
basal ganglion3.74e-089
nuclear complex of neuraxis3.74e-089
aggregate regional part of brain3.74e-089
collection of basal ganglia3.74e-089
cerebral subcortex3.74e-089
hepatic diverticulum5.05e-0822
liver primordium5.05e-0822
trunk region element7.52e-08107
ectoderm-derived structure9.45e-08169
sac9.88e-0826
abdominal segment of trunk1.41e-0761
abdomen1.41e-0761
ectoderm1.84e-07173
presumptive ectoderm1.84e-07173
epithelial sac2.09e-0725
organ part4.12e-07219
telencephalic nucleus7.29e-077
Disease
Ontology termp-valuen
ovarian cancer3.28e-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.