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Coexpression cluster:C1645: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.13e-32!94;UBERON:0001016!4.13e-32!94;UBERON:0005743!6.09e-30!86;UBERON:0004121!2.02e-29!169;UBERON:0003075!4.92e-29!86;UBERON:0007284!4.92e-29!86;UBERON:0001049!7.75e-29!57;UBERON:0005068!7.75e-29!57;UBERON:0006241!7.75e-29!57;UBERON:0007135!7.75e-29!57;UBERON:0001017!8.10e-29!82;UBERON:0000924!4.35e-27!173;UBERON:0006601!4.35e-27!173;UBERON:0002616!3.18e-26!59;UBERON:0002346!1.37e-25!90;UBERON:0000475!1.05e-24!365;UBERON:0003056!2.24e-24!61;UBERON:0000033!1.70e-23!123;UBERON:0000955!5.09e-23!69;UBERON:0006238!5.09e-23!69;UBERON:0000153!6.26e-23!129;UBERON:0007811!6.26e-23!129;UBERON:0002780!4.10e-22!41;UBERON:0001890!4.10e-22!41;UBERON:0006240!4.10e-22!41;UBERON:0003080!8.77e-22!42;UBERON:0002020!4.22e-21!34;UBERON:0003528!4.22e-21!34;UBERON:0001893!8.93e-21!34;UBERON:0002791!3.09e-20!33;UBERON:0001869!4.19e-20!32;UBERON:0000956!1.20e-16!25;UBERON:0000203!1.20e-16!25;UBERON:0000119!4.78e-15!312;UBERON:0002619!8.05e-15!22;UBERON:0000483!1.75e-14!309;UBERON:0007023!5.21e-14!115;UBERON:0001950!1.06e-13!20;UBERON:0000468!6.54e-13!659;UBERON:0000481!1.60e-12!347;UBERON:0000064!5.50e-12!219;UBERON:0000467!2.13e-11!625;UBERON:0000480!3.59e-11!626;UBERON:0000922!1.42e-09!612;UBERON:0002050!1.56e-08!605;UBERON:0005423!1.56e-08!605;UBERON:0000025!2.57e-08!194;UBERON:0000923!2.88e-08!604;UBERON:0005291!2.88e-08!604;UBERON:0006598!2.88e-08!604;UBERON:0002532!2.88e-08!604;UBERON:0003076!3.52e-08!15;UBERON:0003057!3.52e-08!15;UBERON:0000914!2.39e-07!83;UBERON:0002329!2.39e-07!83;UBERON:0003077!2.39e-07!83;UBERON:0003059!2.39e-07!83;UBERON:0007282!2.39e-07!83;UBERON:0009618!2.39e-07!83;UBERON:0007285!2.39e-07!83;UBERON:0004290!3.05e-07!70
|ontology_enrichment_uberon=UBERON:0000073!4.13e-32!94;UBERON:0001016!4.13e-32!94;UBERON:0005743!6.09e-30!86;UBERON:0004121!2.02e-29!169;UBERON:0003075!4.92e-29!86;UBERON:0007284!4.92e-29!86;UBERON:0001049!7.75e-29!57;UBERON:0005068!7.75e-29!57;UBERON:0006241!7.75e-29!57;UBERON:0007135!7.75e-29!57;UBERON:0001017!8.10e-29!82;UBERON:0000924!4.35e-27!173;UBERON:0006601!4.35e-27!173;UBERON:0002616!3.18e-26!59;UBERON:0002346!1.37e-25!90;UBERON:0000475!1.05e-24!365;UBERON:0003056!2.24e-24!61;UBERON:0000033!1.70e-23!123;UBERON:0000955!5.09e-23!69;UBERON:0006238!5.09e-23!69;UBERON:0000153!6.26e-23!129;UBERON:0007811!6.26e-23!129;UBERON:0002780!4.10e-22!41;UBERON:0001890!4.10e-22!41;UBERON:0006240!4.10e-22!41;UBERON:0003080!8.77e-22!42;UBERON:0002020!4.22e-21!34;UBERON:0003528!4.22e-21!34;UBERON:0001893!8.93e-21!34;UBERON:0002791!3.09e-20!33;UBERON:0001869!4.19e-20!32;UBERON:0000956!1.20e-16!25;UBERON:0000203!1.20e-16!25;UBERON:0000119!4.78e-15!312;UBERON:0002619!8.05e-15!22;UBERON:0000483!1.75e-14!309;UBERON:0007023!5.21e-14!115;UBERON:0001950!1.06e-13!20;UBERON:0000468!6.54e-13!659;UBERON:0000481!1.60e-12!347;UBERON:0000064!5.50e-12!219;UBERON:0000467!2.13e-11!625;UBERON:0000480!3.59e-11!626;UBERON:0000922!1.42e-09!612;UBERON:0002050!1.56e-08!605;UBERON:0005423!1.56e-08!605;UBERON:0000025!2.57e-08!194;UBERON:0000923!2.88e-08!604;UBERON:0005291!2.88e-08!604;UBERON:0006598!2.88e-08!604;UBERON:0002532!2.88e-08!604;UBERON:0003076!3.52e-08!15;UBERON:0003057!3.52e-08!15;UBERON:0000914!2.39e-07!83;UBERON:0002329!2.39e-07!83;UBERON:0003077!2.39e-07!83;UBERON:0003059!2.39e-07!83;UBERON:0007282!2.39e-07!83;UBERON:0009618!2.39e-07!83;UBERON:0007285!2.39e-07!83;UBERON:0004290!3.05e-07!70
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00249478501128282!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352290387428697!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276251388417541!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000229220683106164!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714051080610836
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}}
}}

Revision as of 14:14, 5 September 2012


Full id: C1645_temporal_non_occipital_parietal_duodenum_neuroblastoma_brain



Phase1 CAGE Peaks

Hg19::chr11:79151822..79151890,-p1@ODZ4
Hg19::chr11:79151896..79151911,-p8@ODZ4
Hg19::chr11:79151994..79152022,-p2@ODZ4
Hg19::chr11:79152025..79152047,-p5@ODZ4
Hg19::chr11:79152060..79152082,-p4@ODZ4


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><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.64e-11180
electrically responsive cell1.55e-0760
electrically active cell1.55e-0760
contractile cell4.55e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.13e-3294
nervous system4.13e-3294
ectoderm-derived structure2.02e-29169
neural plate4.92e-2986
presumptive neural plate4.92e-2986
neural tube7.75e-2957
neural rod7.75e-2957
future spinal cord7.75e-2957
neural keel7.75e-2957
central nervous system8.10e-2982
ectoderm4.35e-27173
presumptive ectoderm4.35e-27173
regional part of brain3.18e-2659
neurectoderm1.37e-2590
organism subdivision1.05e-24365
pre-chordal neural plate2.24e-2461
head1.70e-23123
brain5.09e-2369
future brain5.09e-2369
anterior region of body6.26e-23129
craniocervical region6.26e-23129
regional part of forebrain4.10e-2241
forebrain4.10e-2241
future forebrain4.10e-2241
anterior neural tube8.77e-2242
gray matter4.22e-2134
brain grey matter4.22e-2134
telencephalon8.93e-2134
regional part of telencephalon3.09e-2033
cerebral hemisphere4.19e-2032
cerebral cortex1.20e-1625
pallium1.20e-1625
cell layer4.78e-15312
regional part of cerebral cortex8.05e-1522
epithelium1.75e-14309
adult organism5.21e-14115
neocortex1.06e-1320
multi-cellular organism6.54e-13659
multi-tissue structure1.60e-12347
organ part5.50e-12219
anatomical system2.13e-11625
anatomical group3.59e-11626
embryo1.42e-09612
embryonic structure1.56e-08605
developing anatomical structure1.56e-08605
tube2.57e-08194
germ layer2.88e-08604
embryonic tissue2.88e-08604
presumptive structure2.88e-08604
epiblast (generic)2.88e-08604
posterior neural tube3.52e-0815
chordal neural plate3.52e-0815
somite2.39e-0783
paraxial mesoderm2.39e-0783
presomitic mesoderm2.39e-0783
presumptive segmental plate2.39e-0783
trunk paraxial mesoderm2.39e-0783
presumptive paraxial mesoderm2.39e-0783
dermomyotome3.05e-0770


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
CTCF#1066455.360256373075030.0002259278299937090.00249478501128282
E2F1#186954.907389214879320.0003512818099256460.00352290387428697
MYC#460955.22228187160940.0002573944848850610.00276251388417541
RAD21#5885510.35503389545638.39503550283973e-060.000229220683106164
SPI1#668846.563458806818180.0009957429636454020.00714051080610836



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.