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Coexpression cluster:C4557: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.16e-22!115;UBERON:0001049!1.06e-20!57;UBERON:0005068!1.06e-20!57;UBERON:0006241!1.06e-20!57;UBERON:0007135!1.06e-20!57;UBERON:0003080!6.63e-19!42;UBERON:0002780!1.61e-18!41;UBERON:0001890!1.61e-18!41;UBERON:0006240!1.61e-18!41;UBERON:0002346!1.33e-17!90;UBERON:0001017!3.11e-17!82;UBERON:0000955!7.08e-17!69;UBERON:0006238!7.08e-17!69;UBERON:0002020!7.68e-17!34;UBERON:0003528!7.68e-17!34;UBERON:0001893!1.50e-16!34;UBERON:0002616!1.89e-16!59;UBERON:0005743!3.86e-16!86;UBERON:0002791!4.07e-16!33;UBERON:0003075!7.73e-16!86;UBERON:0007284!7.73e-16!86;UBERON:0000073!1.00e-15!94;UBERON:0001016!1.00e-15!94;UBERON:0001869!1.88e-15!32;UBERON:0000956!1.24e-11!25;UBERON:0000203!1.24e-11!25;UBERON:0002619!2.33e-11!22;UBERON:0003056!4.83e-11!61;UBERON:0001950!3.59e-10!20;UBERON:0000924!4.00e-08!173;UBERON:0006601!4.00e-08!173;UBERON:0000033!3.45e-07!123;UBERON:0004121!4.35e-07!169;UBERON:0000153!5.06e-07!129;UBERON:0007811!5.06e-07!129;UBERON:0002308!7.93e-07!9;UBERON:0000125!7.93e-07!9;UBERON:0002420!9.96e-07!9;UBERON:0007245!9.96e-07!9;UBERON:0010009!9.96e-07!9;UBERON:0010011!9.96e-07!9;UBERON:0000454!9.96e-07!9
|ontology_enrichment_uberon=UBERON:0007023!4.16e-22!115;UBERON:0001049!1.06e-20!57;UBERON:0005068!1.06e-20!57;UBERON:0006241!1.06e-20!57;UBERON:0007135!1.06e-20!57;UBERON:0003080!6.63e-19!42;UBERON:0002780!1.61e-18!41;UBERON:0001890!1.61e-18!41;UBERON:0006240!1.61e-18!41;UBERON:0002346!1.33e-17!90;UBERON:0001017!3.11e-17!82;UBERON:0000955!7.08e-17!69;UBERON:0006238!7.08e-17!69;UBERON:0002020!7.68e-17!34;UBERON:0003528!7.68e-17!34;UBERON:0001893!1.50e-16!34;UBERON:0002616!1.89e-16!59;UBERON:0005743!3.86e-16!86;UBERON:0002791!4.07e-16!33;UBERON:0003075!7.73e-16!86;UBERON:0007284!7.73e-16!86;UBERON:0000073!1.00e-15!94;UBERON:0001016!1.00e-15!94;UBERON:0001869!1.88e-15!32;UBERON:0000956!1.24e-11!25;UBERON:0000203!1.24e-11!25;UBERON:0002619!2.33e-11!22;UBERON:0003056!4.83e-11!61;UBERON:0001950!3.59e-10!20;UBERON:0000924!4.00e-08!173;UBERON:0006601!4.00e-08!173;UBERON:0000033!3.45e-07!123;UBERON:0004121!4.35e-07!169;UBERON:0000153!5.06e-07!129;UBERON:0007811!5.06e-07!129;UBERON:0002308!7.93e-07!9;UBERON:0000125!7.93e-07!9;UBERON:0002420!9.96e-07!9;UBERON:0007245!9.96e-07!9;UBERON:0010009!9.96e-07!9;UBERON:0010011!9.96e-07!9;UBERON:0000454!9.96e-07!9
|tf_chipseq_enrich=TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197837688624353
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}}
}}

Revision as of 13:10, 5 September 2012


Full id: C4557_eye_olfactory_spinal_thalamus_testicular_putamen_Cardiac



Phase1 CAGE Peaks

Hg19::chr6:131277237..131277257,-p7@EPB41L2
Hg19::chr6:131277274..131277298,-p8@EPB41L2
Hg19::chr6:131277349..131277414,-p3@EPB41L2


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 organism4.16e-22115
neural tube1.06e-2057
neural rod1.06e-2057
future spinal cord1.06e-2057
neural keel1.06e-2057
anterior neural tube6.63e-1942
regional part of forebrain1.61e-1841
forebrain1.61e-1841
future forebrain1.61e-1841
neurectoderm1.33e-1790
central nervous system3.11e-1782
brain7.08e-1769
future brain7.08e-1769
gray matter7.68e-1734
brain grey matter7.68e-1734
telencephalon1.50e-1634
regional part of brain1.89e-1659
regional part of telencephalon4.07e-1633
neural plate7.73e-1686
presumptive neural plate7.73e-1686
regional part of nervous system1.00e-1594
nervous system1.00e-1594
cerebral hemisphere1.88e-1532
cerebral cortex1.24e-1125
pallium1.24e-1125
regional part of cerebral cortex2.33e-1122
pre-chordal neural plate4.83e-1161
neocortex3.59e-1020
ectoderm4.00e-08173
presumptive ectoderm4.00e-08173
head3.45e-07123
ectoderm-derived structure4.35e-07169
anterior region of body5.06e-07129
craniocervical region5.06e-07129
nucleus of brain7.93e-079
neural nucleus7.93e-079
basal ganglion9.96e-079
nuclear complex of neuraxis9.96e-079
aggregate regional part of brain9.96e-079
collection of basal ganglia9.96e-079
cerebral subcortex9.96e-079


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
TRIM28#10155318.59052504526250.0001555969297255280.00197837688624353



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.