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Coexpression cluster:C652: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!4.02e-53!115;UBERON:0001049!3.68e-29!57;UBERON:0005068!3.68e-29!57;UBERON:0006241!3.68e-29!57;UBERON:0007135!3.68e-29!57;UBERON:0001017!2.96e-28!82;UBERON:0000073!8.63e-28!94;UBERON:0001016!8.63e-28!94;UBERON:0005743!1.06e-27!86;UBERON:0003080!1.29e-24!42;UBERON:0002780!2.19e-24!41;UBERON:0001890!2.19e-24!41;UBERON:0006240!2.19e-24!41;UBERON:0002616!4.16e-24!59;UBERON:0000955!6.78e-24!69;UBERON:0006238!6.78e-24!69;UBERON:0001893!7.02e-20!34;UBERON:0002020!7.33e-20!34;UBERON:0003528!7.33e-20!34;UBERON:0002346!1.19e-19!90;UBERON:0003075!2.46e-19!86;UBERON:0007284!2.46e-19!86;UBERON:0002791!3.11e-19!33;UBERON:0001869!9.18e-19!32;UBERON:0002619!1.87e-15!22;UBERON:0003056!9.99e-15!61;UBERON:0000956!1.87e-14!25;UBERON:0000203!1.87e-14!25;UBERON:0000153!2.04e-14!129;UBERON:0007811!2.04e-14!129;UBERON:0001950!3.17e-14!20;UBERON:0000924!6.31e-14!173;UBERON:0006601!6.31e-14!173;UBERON:0004121!1.69e-13!169;UBERON:0000033!5.69e-13!123;UBERON:0002420!5.05e-07!9;UBERON:0007245!5.05e-07!9;UBERON:0010009!5.05e-07!9;UBERON:0010011!5.05e-07!9;UBERON:0000454!5.05e-07!9;UBERON:0002308!6.71e-07!9;UBERON:0000125!6.71e-07!9
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}}
}}

Revision as of 20:39, 8 August 2012


Full id: C652_cerebellum_occipital_pineal_pituitary_medial_parietal_amygdala



Phase1 CAGE Peaks

Hg19::chr11:105948040..105948082,-p1@KBTBD3
Hg19::chr11:8190534..8190595,-p1@RIC3
Hg19::chr17:40897043..40897087,-p1@EZH1
Hg19::chr17:5095296..5095308,+p2@LOC100130950
Hg19::chr19:38085739..38085762,+p3@ZNF540
Hg19::chr19:38085768..38085821,+p1@ZNF540
Hg19::chr1:244998602..244998646,+p3@FAM36A
Hg19::chr3:108308331..108308389,+p2@DZIP3
Hg19::chr4:149363637..149363651,-p4@NR3C2
Hg19::chr4:149363662..149363688,-p6@NR3C2
Hg19::chr6:117002339..117002400,+p1@KPNA5
Hg19::chr6:27342978..27343050,-p1@ZNF204P
Hg19::chr8:119634141..119634223,-p1@SAMD12


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


GO IDGO nameFDR corrected p-value
GO:0031593polyubiquitin binding0.0282241442524776
GO:0055078sodium ion homeostasis0.0282241442524776
GO:0006883cellular sodium ion homeostasis0.0282241442524776
GO:0012505endomembrane system0.0302301958653872
GO:0000209protein polyubiquitination0.0398664843190308
GO:0006607NLS-bearing substrate import into nucleus0.0398664843190308
GO:0031090organelle membrane0.0398664843190308
GO:0030004cellular monovalent inorganic cation homeostasis0.0398664843190308
GO:0055067monovalent inorganic cation homeostasis0.0398664843190308
GO:0043130ubiquitin binding0.0398664843190308
GO:0032182small conjugating protein binding0.0398664843190308
GO:0005789endoplasmic reticulum membrane0.0398664843190308
GO:0042175nuclear envelope-endoplasmic reticulum network0.0398664843190308
GO:0044432endoplasmic reticulum part0.0456690194223664



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>


Uber Anatomy
Ontology termp-valuen
adult organism4.02e-53115
neural tube3.68e-2957
neural rod3.68e-2957
future spinal cord3.68e-2957
neural keel3.68e-2957
central nervous system2.96e-2882
regional part of nervous system8.63e-2894
nervous system8.63e-2894
anterior neural tube1.29e-2442
regional part of forebrain2.19e-2441
forebrain2.19e-2441
future forebrain2.19e-2441
regional part of brain4.16e-2459
brain6.78e-2469
future brain6.78e-2469
telencephalon7.02e-2034
gray matter7.33e-2034
brain grey matter7.33e-2034
neurectoderm1.19e-1990
neural plate2.46e-1986
presumptive neural plate2.46e-1986
regional part of telencephalon3.11e-1933
cerebral hemisphere9.18e-1932
regional part of cerebral cortex1.87e-1522
pre-chordal neural plate9.99e-1561
cerebral cortex1.87e-1425
pallium1.87e-1425
anterior region of body2.04e-14129
craniocervical region2.04e-14129
neocortex3.17e-1420
ectoderm6.31e-14173
presumptive ectoderm6.31e-14173
ectoderm-derived structure1.69e-13169
head5.69e-13123
basal ganglion5.05e-079
nuclear complex of neuraxis5.05e-079
aggregate regional part of brain5.05e-079
collection of basal ganglia5.05e-079
cerebral subcortex5.05e-079
nucleus of brain6.71e-079
neural nucleus6.71e-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)

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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


No analysis results for this cluster

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.