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Coexpression cluster:C702: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.72e-41!94;UBERON:0001016!1.72e-41!94;UBERON:0005743!4.14e-40!86;UBERON:0001017!3.79e-39!82;UBERON:0007023!1.43e-38!115;UBERON:0001049!5.30e-37!57;UBERON:0005068!5.30e-37!57;UBERON:0006241!5.30e-37!57;UBERON:0007135!5.30e-37!57;UBERON:0004121!4.62e-35!169;UBERON:0000924!2.50e-34!173;UBERON:0006601!2.50e-34!173;UBERON:0003075!1.21e-33!86;UBERON:0007284!1.21e-33!86;UBERON:0002346!3.40e-32!90;UBERON:0002616!1.73e-31!59;UBERON:0000955!8.17e-31!69;UBERON:0006238!8.17e-31!69;UBERON:0003080!3.87e-28!42;UBERON:0002780!9.28e-28!41;UBERON:0001890!9.28e-28!41;UBERON:0006240!9.28e-28!41;UBERON:0000033!1.16e-27!123;UBERON:0000153!1.29e-27!129;UBERON:0007811!1.29e-27!129;UBERON:0002020!7.73e-24!34;UBERON:0003528!7.73e-24!34;UBERON:0003056!8.70e-24!61;UBERON:0001893!1.22e-23!34;UBERON:0002791!4.93e-23!33;UBERON:0001869!2.20e-22!32;UBERON:0000956!8.07e-18!25;UBERON:0000203!8.07e-18!25;UBERON:0002619!3.91e-16!22;UBERON:0001950!1.00e-14!20;UBERON:0000922!1.08e-13!612;UBERON:0000475!3.20e-13!365;UBERON:0000062!2.85e-12!511;UBERON:0000468!6.77e-12!659;UBERON:0002050!3.21e-11!605;UBERON:0005423!3.21e-11!605;UBERON:0000923!6.46e-11!604;UBERON:0005291!6.46e-11!604;UBERON:0006598!6.46e-11!604;UBERON:0002532!6.46e-11!604;UBERON:0000480!7.82e-11!626;UBERON:0000467!8.54e-11!625;UBERON:0000481!7.25e-10!347;UBERON:0003076!7.46e-10!15;UBERON:0003057!7.46e-10!15;UBERON:0000064!1.31e-09!219;UBERON:0000483!2.03e-08!309;UBERON:0004732!2.40e-08!13;UBERON:0004111!2.42e-08!241;UBERON:0000025!3.60e-08!194;UBERON:0000119!3.67e-08!312;UBERON:0004733!8.60e-08!12;UBERON:0002028!8.60e-08!12;UBERON:0007277!8.60e-08!12;UBERON:0002308!1.84e-07!9;UBERON:0000125!1.84e-07!9;UBERON:0002420!2.16e-07!9;UBERON:0007245!2.16e-07!9;UBERON:0010009!2.16e-07!9;UBERON:0010011!2.16e-07!9;UBERON:0000454!2.16e-07!9
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}}
}}

Revision as of 20:43, 8 August 2012


Full id: C702_spinal_parietal_Neural_occipital_locus_temporal_globus



Phase1 CAGE Peaks

Hg19::chr15:93632421..93632446,-p1@RGMA
Hg19::chr16:72459838..72459857,+p1@uc002fch.1
Hg19::chr17:49124054..49124065,-p8@SPAG9
Hg19::chr17:54230819..54230848,+p1@ANKFN1
Hg19::chr19:51814892..51814930,+p1@IGLON5
Hg19::chr6:123154483..123154508,-p@chr6:123154483..123154508
-
Hg19::chr7:103969251..103969288,+p1@LHFPL3
Hg19::chr7:121513146..121513153,+p3@PTPRZ1
Hg19::chr7:121513171..121513202,+p2@PTPRZ1
Hg19::chr7:121513207..121513221,+p1@PTPRZ1
Hg19::chr8:63161180..63161204,+p4@NKAIN3
Hg19::chr8:85618155..85618173,+p3@RALYL


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:0001843neural tube closure0.0357467999751478
GO:0014020primary neural tube formation0.0357467999751478
GO:0001839neural plate morphogenesis0.0357467999751478
GO:0001841neural tube formation0.0357467999751478
GO:0001840neural plate development0.0357467999751478
GO:0001838embryonic epithelial tube formation0.0357467999751478
GO:0019198transmembrane receptor protein phosphatase activity0.0357467999751478
GO:0021915neural tube development0.0357467999751478
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0357467999751478
GO:0016331morphogenesis of embryonic epithelium0.0369304705862911
GO:0001669acrosome0.0369304705862911



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
neural cell1.30e-0725
ectodermal cell2.40e-0771
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.72e-4194
nervous system1.72e-4194
central nervous system3.79e-3982
adult organism1.43e-38115
neural tube5.30e-3757
neural rod5.30e-3757
future spinal cord5.30e-3757
neural keel5.30e-3757
ectoderm-derived structure4.62e-35169
ectoderm2.50e-34173
presumptive ectoderm2.50e-34173
neural plate1.21e-3386
presumptive neural plate1.21e-3386
neurectoderm3.40e-3290
regional part of brain1.73e-3159
brain8.17e-3169
future brain8.17e-3169
anterior neural tube3.87e-2842
regional part of forebrain9.28e-2841
forebrain9.28e-2841
future forebrain9.28e-2841
head1.16e-27123
anterior region of body1.29e-27129
craniocervical region1.29e-27129
gray matter7.73e-2434
brain grey matter7.73e-2434
pre-chordal neural plate8.70e-2461
telencephalon1.22e-2334
regional part of telencephalon4.93e-2333
cerebral hemisphere2.20e-2232
cerebral cortex8.07e-1825
pallium8.07e-1825
regional part of cerebral cortex3.91e-1622
neocortex1.00e-1420
embryo1.08e-13612
organism subdivision3.20e-13365
organ2.85e-12511
multi-cellular organism6.77e-12659
embryonic structure3.21e-11605
developing anatomical structure3.21e-11605
germ layer6.46e-11604
embryonic tissue6.46e-11604
presumptive structure6.46e-11604
epiblast (generic)6.46e-11604
anatomical group7.82e-11626
anatomical system8.54e-11625
multi-tissue structure7.25e-10347
posterior neural tube7.46e-1015
chordal neural plate7.46e-1015
organ part1.31e-09219
epithelium2.03e-08309
segmental subdivision of nervous system2.40e-0813
anatomical conduit2.42e-08241
tube3.60e-08194
cell layer3.67e-08312
segmental subdivision of hindbrain8.60e-0812
hindbrain8.60e-0812
presumptive hindbrain8.60e-0812
nucleus of brain1.84e-079
neural nucleus1.84e-079
basal ganglion2.16e-079
nuclear complex of neuraxis2.16e-079
aggregate regional part of brain2.16e-079
collection of basal ganglia2.16e-079
cerebral subcortex2.16e-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.