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Coexpression cluster:C4381: Difference between revisions

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|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!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
|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 13:50, 5 September 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 organism6.96e-62115
neural tube1.16e-2557
neural rod1.16e-2557
future spinal cord1.16e-2557
neural keel1.16e-2557
neural plate1.01e-2186
presumptive neural plate1.01e-2186
neurectoderm9.69e-2190
regional part of brain5.45e-2059
anterior neural tube7.64e-2042
regional part of nervous system8.59e-2094
nervous system8.59e-2094
brain2.69e-1969
future brain2.69e-1969
regional part of forebrain4.26e-1941
forebrain4.26e-1941
future forebrain4.26e-1941
central nervous system4.61e-1982
telencephalon2.28e-1734
gray matter4.09e-1734
brain grey matter4.09e-1734
regional part of telencephalon9.09e-1733
cerebral hemisphere1.88e-1632
pre-chordal neural plate9.61e-1661
ectoderm-derived structure2.73e-13169
regional part of cerebral cortex4.95e-1322
ectoderm5.67e-13173
presumptive ectoderm5.67e-13173
anterior region of body3.81e-12129
craniocervical region3.81e-12129
neocortex4.09e-1220
cerebral cortex5.13e-1225
pallium5.13e-1225
head2.00e-11123
tube8.73e-09194
anatomical conduit7.19e-08241
organ part4.63e-07219
posterior neural tube5.07e-0715
chordal neural plate5.07e-0715
basal ganglion6.11e-079
nuclear complex of neuraxis6.11e-079
aggregate regional part of brain6.11e-079
collection of basal ganglia6.11e-079
cerebral subcortex6.11e-079
anatomical cluster6.59e-07286


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.

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