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Coexpression cluster:C2426: Difference between revisions

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|full_id=C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal
|full_id=C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal
|id=C2426
|id=C2426
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000784!2.35e-07!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!9.65e-50!57;UBERON:0005068!9.65e-50!57;UBERON:0006241!9.65e-50!57;UBERON:0007135!9.65e-50!57;UBERON:0001017!7.83e-44!82;UBERON:0000955!1.19e-43!69;UBERON:0006238!1.19e-43!69;UBERON:0005743!1.48e-42!86;UBERON:0002616!3.58e-42!59;UBERON:0000073!1.13e-40!94;UBERON:0001016!1.13e-40!94;UBERON:0002780!2.42e-40!41;UBERON:0001890!2.42e-40!41;UBERON:0006240!2.42e-40!41;UBERON:0007023!5.61e-40!115;UBERON:0003080!4.74e-39!42;UBERON:0002346!4.16e-35!90;UBERON:0003075!8.25e-35!86;UBERON:0007284!8.25e-35!86;UBERON:0002020!6.39e-33!34;UBERON:0003528!6.39e-33!34;UBERON:0001893!8.03e-33!34;UBERON:0002791!1.62e-31!33;UBERON:0001869!2.19e-30!32;UBERON:0003056!2.11e-25!61;UBERON:0000033!9.42e-23!123;UBERON:0002619!1.60e-22!22;UBERON:0000956!2.23e-22!25;UBERON:0000203!2.23e-22!25;UBERON:0000153!9.95e-22!129;UBERON:0007811!9.95e-22!129;UBERON:0000924!7.67e-21!173;UBERON:0006601!7.67e-21!173;UBERON:0001950!1.41e-20!20;UBERON:0004121!3.03e-20!169;UBERON:0002308!3.83e-12!9;UBERON:0000125!3.83e-12!9;UBERON:0003076!1.43e-11!15;UBERON:0003057!1.43e-11!15;UBERON:0000025!7.14e-11!194;UBERON:0009663!1.68e-09!7;UBERON:0004732!3.11e-09!13;UBERON:0002420!3.70e-09!9;UBERON:0007245!3.70e-09!9;UBERON:0010009!3.70e-09!9;UBERON:0010011!3.70e-09!9;UBERON:0000454!3.70e-09!9;UBERON:0002298!4.19e-09!8;UBERON:0000200!4.21e-09!6;UBERON:0004111!5.35e-09!241;UBERON:0001894!7.39e-09!7;UBERON:0006222!7.39e-09!7;UBERON:0004733!3.66e-08!12;UBERON:0002028!3.66e-08!12;UBERON:0007277!3.66e-08!12;UBERON:0001871!5.81e-08!7;UBERON:0000475!1.40e-07!365;UBERON:0000477!1.53e-07!286;UBERON:0002021!3.43e-07!5;UBERON:0000062!3.81e-07!511
|ontology_enrichment_uberon=UBERON:0001049!2.13e-53!56;UBERON:0005068!2.13e-53!56;UBERON:0006241!2.13e-53!56;UBERON:0007135!2.13e-53!56;UBERON:0001017!4.58e-50!81;UBERON:0000073!5.84e-48!53;UBERON:0002616!5.84e-48!53;UBERON:0000955!4.20e-47!68;UBERON:0006238!4.20e-47!68;UBERON:0001016!1.24e-45!89;UBERON:0002780!1.70e-41!41;UBERON:0001890!1.70e-41!41;UBERON:0003080!1.70e-41!41;UBERON:0006240!1.70e-41!41;UBERON:0003075!8.51e-38!82;UBERON:0007284!8.51e-38!82;UBERON:0002346!3.41e-37!86;UBERON:0003528!3.67e-36!34;UBERON:0002020!3.67e-36!34;UBERON:0001893!5.23e-36!34;UBERON:0007023!4.38e-33!114;UBERON:0001869!1.05e-32!32;UBERON:0002791!1.76e-32!32;UBERON:0003056!3.33e-30!61;UBERON:0010371!3.53e-30!104;UBERON:0002619!3.64e-25!22;UBERON:0001950!5.33e-25!20;UBERON:0010314!7.16e-24!132;UBERON:0004121!9.08e-24!171;UBERON:0000924!9.08e-24!171;UBERON:0006601!9.08e-24!171;UBERON:0000956!1.30e-21!25;UBERON:0000203!1.30e-21!25;UBERON:0000125!3.98e-17!9;UBERON:0002308!3.98e-17!9;UBERON:0011216!1.40e-16!223;UBERON:0002298!1.69e-13!6;UBERON:0009663!3.27e-13!7;UBERON:0002420!5.20e-13!9;UBERON:0007245!5.20e-13!9;UBERON:0010009!5.20e-13!9;UBERON:0010011!5.20e-13!9;UBERON:0000454!5.20e-13!9;UBERON:0000200!8.64e-13!6;UBERON:0003076!1.05e-12!15;UBERON:0003057!1.05e-12!15;UBERON:0000025!2.40e-11!192;UBERON:0004732!2.59e-09!13;UBERON:0000369!2.87e-08!4;UBERON:0002435!2.87e-08!4;UBERON:0000204!2.87e-08!4;UBERON:0010082!2.87e-08!4;UBERON:0004733!5.71e-08!12;UBERON:0002028!5.71e-08!12;UBERON:0007277!5.71e-08!12;UBERON:0000988!1.16e-07!3;UBERON:0004111!1.26e-07!240;UBERON:0001896!1.69e-07!3;UBERON:0005290!1.69e-07!3;UBERON:0010096!1.69e-07!3;UBERON:0002240!2.16e-07!3;UBERON:0005174!2.16e-07!3;UBERON:0001137!2.16e-07!3;UBERON:0002021!3.25e-07!5;UBERON:0001872!3.46e-07!5;UBERON:0001870!3.99e-07!3;UBERON:0001871!4.99e-07!6;UBERON:0001894!7.10e-07!7;UBERON:0006222!7.10e-07!7
|tf_chipseq_enrich=MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088736145198388!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106807823959729
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}}
}}

Revision as of 14:00, 19 October 2012


Full id: C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal



Phase1 CAGE Peaks

Hg19::chr17:61116852..61116863,+p4@AB074278
Hg19::chr17:61116864..61116883,+p3@AB074278
Hg19::chr17:61116885..61116914,+p1@AB074278
Hg19::chr17:61116919..61116955,+p2@AB074278


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
plasmacytoid dendritic cell2.35e-073
Uber Anatomy
Ontology termp-valuen
neural tube2.13e-5356
neural rod2.13e-5356
future spinal cord2.13e-5356
neural keel2.13e-5356
central nervous system4.58e-5081
regional part of nervous system5.84e-4853
regional part of brain5.84e-4853
brain4.20e-4768
future brain4.20e-4768
nervous system1.24e-4589
regional part of forebrain1.70e-4141
forebrain1.70e-4141
anterior neural tube1.70e-4141
future forebrain1.70e-4141
neural plate8.51e-3882
presumptive neural plate8.51e-3882
neurectoderm3.41e-3786
brain grey matter3.67e-3634
gray matter3.67e-3634
telencephalon5.23e-3634
adult organism4.38e-33114
cerebral hemisphere1.05e-3232
regional part of telencephalon1.76e-3232
pre-chordal neural plate3.33e-3061
ecto-epithelium3.53e-30104
regional part of cerebral cortex3.64e-2522
neocortex5.33e-2520
structure with developmental contribution from neural crest7.16e-24132
ectoderm-derived structure9.08e-24171
ectoderm9.08e-24171
presumptive ectoderm9.08e-24171
cerebral cortex1.30e-2125
pallium1.30e-2125
neural nucleus3.98e-179
nucleus of brain3.98e-179
organ system subdivision1.40e-16223
brainstem1.69e-136
telencephalic nucleus3.27e-137
basal ganglion5.20e-139
nuclear complex of neuraxis5.20e-139
aggregate regional part of brain5.20e-139
collection of basal ganglia5.20e-139
cerebral subcortex5.20e-139
gyrus8.64e-136
posterior neural tube1.05e-1215
chordal neural plate1.05e-1215
tube2.40e-11192
segmental subdivision of nervous system2.59e-0913
corpus striatum2.87e-084
striatum2.87e-084
ventral part of telencephalon2.87e-084
future corpus striatum2.87e-084
segmental subdivision of hindbrain5.71e-0812
hindbrain5.71e-0812
presumptive hindbrain5.71e-0812
pons1.16e-073
anatomical conduit1.26e-07240
medulla oblongata1.69e-073
myelencephalon1.69e-073
future myelencephalon1.69e-073
spinal cord2.16e-073
dorsal region element2.16e-073
dorsum2.16e-073
occipital lobe3.25e-075
parietal lobe3.46e-075
frontal cortex3.99e-073
temporal lobe4.99e-076
diencephalon7.10e-077
future diencephalon7.10e-077


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
MYC#460945.22228187160940.001344309395272740.0088736145198388
YY1#752844.911170749853860.00171871838055440.0106807823959729



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.