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Coexpression cluster:C4381: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.96e-62!115;UBERON:0001049!1.16e-25!57;UBERON:0005068!1.16e-25!57;UBERON:0006241!1.16e-25!57;UBERON:0007135!1.16e-25!57;UBERON:0003075!1.01e-21!86;UBERON:0007284!1.01e-21!86;UBERON:0002346!9.69e-21!90;UBERON:0002616!5.45e-20!59;UBERON:0003080!7.64e-20!42;UBERON:0000073!8.59e-20!94;UBERON:0001016!8.59e-20!94;UBERON:0005743!1.60e-19!86;UBERON:0000955!2.69e-19!69;UBERON:0006238!2.69e-19!69;UBERON:0002780!4.26e-19!41;UBERON:0001890!4.26e-19!41;UBERON:0006240!4.26e-19!41;UBERON:0001017!4.61e-19!82;UBERON:0001893!2.28e-17!34;UBERON:0002020!4.09e-17!34;UBERON:0003528!4.09e-17!34;UBERON:0002791!9.09e-17!33;UBERON:0001869!1.88e-16!32;UBERON:0003056!9.61e-16!61;UBERON:0004121!2.73e-13!169;UBERON:0002619!4.95e-13!22;UBERON:0000924!5.67e-13!173;UBERON:0006601!5.67e-13!173;UBERON:0000153!3.81e-12!129;UBERON:0007811!3.81e-12!129;UBERON:0001950!4.09e-12!20;UBERON:0000956!5.13e-12!25;UBERON:0000203!5.13e-12!25;UBERON:0000033!2.00e-11!123;UBERON:0000025!8.73e-09!194;UBERON:0004111!7.19e-08!241;UBERON:0000064!4.63e-07!219;UBERON:0003076!5.07e-07!15;UBERON:0003057!5.07e-07!15;UBERON:0002420!6.11e-07!9;UBERON:0007245!6.11e-07!9;UBERON:0010009!6.11e-07!9;UBERON:0010011!6.11e-07!9;UBERON:0000454!6.11e-07!9;UBERON:0000477!6.59e-07!286
|ontology_enrichment_uberon=UBERON:0007023!8.74e-65!114;UBERON:0001049!1.90e-20!56;UBERON:0005068!1.90e-20!56;UBERON:0006241!1.90e-20!56;UBERON:0007135!1.90e-20!56;UBERON:0003075!1.48e-18!82;UBERON:0007284!1.48e-18!82;UBERON:0000073!2.10e-18!53;UBERON:0002616!2.10e-18!53;UBERON:0002346!7.11e-17!86;UBERON:0001016!7.92e-16!89;UBERON:0000955!1.70e-15!68;UBERON:0006238!1.70e-15!68;UBERON:0002780!1.86e-15!41;UBERON:0001890!1.86e-15!41;UBERON:0003080!1.86e-15!41;UBERON:0006240!1.86e-15!41;UBERON:0001017!2.22e-15!81;UBERON:0001893!4.72e-15!34;UBERON:0003528!6.85e-15!34;UBERON:0002020!6.85e-15!34;UBERON:0001869!5.20e-14!32;UBERON:0002791!9.93e-14!32;UBERON:0010314!1.42e-13!132;UBERON:0011216!2.12e-13!223;UBERON:0003056!4.67e-13!61;UBERON:0010371!4.96e-13!104;UBERON:0001950!4.39e-11!20;UBERON:0002619!7.03e-11!22;UBERON:0004121!2.95e-10!171;UBERON:0000924!2.95e-10!171;UBERON:0006601!2.95e-10!171;UBERON:0000956!6.38e-09!25;UBERON:0000203!6.38e-09!25;UBERON:0000477!1.35e-08!373;UBERON:0002420!2.39e-08!9;UBERON:0007245!2.39e-08!9;UBERON:0010009!2.39e-08!9;UBERON:0010011!2.39e-08!9;UBERON:0000454!2.39e-08!9;UBERON:0000125!3.72e-08!9;UBERON:0002308!3.72e-08!9;UBERON:0000481!1.57e-07!342;UBERON:0000064!4.22e-07!218;UBERON:0009663!5.46e-07!7
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917989579021504!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0063095424170679!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109793927740416
|tf_chipseq_enrich=EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917989579021504!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0063095424170679!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109793927740416
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}}
}}

Revision as of 15:54, 19 October 2012


Full id: C4381_aorta_smallcell_heart_mesodermal_Whole_lung_retina



Phase1 CAGE Peaks

Hg19::chr4:156588806..156588823,+p3@GUCY1A3
Hg19::chr4:156588844..156588864,+p8@GUCY1A3
Hg19::chr4:156588865..156588882,+p6@GUCY1A3


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 organism8.74e-65114
neural tube1.90e-2056
neural rod1.90e-2056
future spinal cord1.90e-2056
neural keel1.90e-2056
neural plate1.48e-1882
presumptive neural plate1.48e-1882
regional part of nervous system2.10e-1853
regional part of brain2.10e-1853
neurectoderm7.11e-1786
nervous system7.92e-1689
brain1.70e-1568
future brain1.70e-1568
regional part of forebrain1.86e-1541
forebrain1.86e-1541
anterior neural tube1.86e-1541
future forebrain1.86e-1541
central nervous system2.22e-1581
telencephalon4.72e-1534
brain grey matter6.85e-1534
gray matter6.85e-1534
cerebral hemisphere5.20e-1432
regional part of telencephalon9.93e-1432
structure with developmental contribution from neural crest1.42e-13132
organ system subdivision2.12e-13223
pre-chordal neural plate4.67e-1361
ecto-epithelium4.96e-13104
neocortex4.39e-1120
regional part of cerebral cortex7.03e-1122
ectoderm-derived structure2.95e-10171
ectoderm2.95e-10171
presumptive ectoderm2.95e-10171
cerebral cortex6.38e-0925
pallium6.38e-0925
anatomical cluster1.35e-08373
basal ganglion2.39e-089
nuclear complex of neuraxis2.39e-089
aggregate regional part of brain2.39e-089
collection of basal ganglia2.39e-089
cerebral subcortex2.39e-089
neural nucleus3.72e-089
nucleus of brain3.72e-089
multi-tissue structure1.57e-07342
organ part4.22e-07218
telencephalic nucleus5.46e-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
EBF1#187938.9064668465690.00141523283560980.00917989579021504
TCF12#6938310.63446490218640.0008313523990202070.0063095424170679
ZNF263#1012738.221841637010680.001799043925565870.0109793927740416



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4381&oldid=2250706"