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Coexpression cluster:C2174: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.36e-40!94;UBERON:0001016!1.36e-40!94;UBERON:0005743!4.46e-40!86;UBERON:0001017!7.44e-39!82;UBERON:0001049!8.35e-34!57;UBERON:0005068!8.35e-34!57;UBERON:0006241!8.35e-34!57;UBERON:0007135!8.35e-34!57;UBERON:0002616!1.88e-30!59;UBERON:0000955!2.10e-30!69;UBERON:0006238!2.10e-30!69;UBERON:0002780!2.60e-28!41;UBERON:0001890!2.60e-28!41;UBERON:0006240!2.60e-28!41;UBERON:0003080!2.80e-28!42;UBERON:0003075!4.25e-28!86;UBERON:0007284!4.25e-28!86;UBERON:0002346!7.27e-28!90;UBERON:0002020!4.62e-25!34;UBERON:0003528!4.62e-25!34;UBERON:0001893!4.88e-25!34;UBERON:0003056!2.62e-24!61;UBERON:0002791!2.81e-24!33;UBERON:0001869!3.01e-24!32;UBERON:0007023!8.41e-23!115;UBERON:0000924!9.01e-21!173;UBERON:0006601!9.01e-21!173;UBERON:0004121!1.40e-20!169;UBERON:0000956!2.75e-19!25;UBERON:0000203!2.75e-19!25;UBERON:0002619!2.83e-17!22;UBERON:0000033!3.49e-17!123;UBERON:0000153!4.24e-17!129;UBERON:0007811!4.24e-17!129;UBERON:0001950!5.61e-16!20;UBERON:0000475!3.85e-13!365;UBERON:0002420!2.65e-07!9;UBERON:0007245!2.65e-07!9;UBERON:0010009!2.65e-07!9;UBERON:0010011!2.65e-07!9;UBERON:0000454!2.65e-07!9;UBERON:0002308!3.26e-07!9;UBERON:0000125!3.26e-07!9;UBERON:0003076!5.82e-07!15;UBERON:0003057!5.82e-07!15;UBERON:0000468!6.15e-07!659
|ontology_enrichment_uberon=UBERON:0000073!1.36e-40!94;UBERON:0001016!1.36e-40!94;UBERON:0005743!4.46e-40!86;UBERON:0001017!7.44e-39!82;UBERON:0001049!8.35e-34!57;UBERON:0005068!8.35e-34!57;UBERON:0006241!8.35e-34!57;UBERON:0007135!8.35e-34!57;UBERON:0002616!1.88e-30!59;UBERON:0000955!2.10e-30!69;UBERON:0006238!2.10e-30!69;UBERON:0002780!2.60e-28!41;UBERON:0001890!2.60e-28!41;UBERON:0006240!2.60e-28!41;UBERON:0003080!2.80e-28!42;UBERON:0003075!4.25e-28!86;UBERON:0007284!4.25e-28!86;UBERON:0002346!7.27e-28!90;UBERON:0002020!4.62e-25!34;UBERON:0003528!4.62e-25!34;UBERON:0001893!4.88e-25!34;UBERON:0003056!2.62e-24!61;UBERON:0002791!2.81e-24!33;UBERON:0001869!3.01e-24!32;UBERON:0007023!8.41e-23!115;UBERON:0000924!9.01e-21!173;UBERON:0006601!9.01e-21!173;UBERON:0004121!1.40e-20!169;UBERON:0000956!2.75e-19!25;UBERON:0000203!2.75e-19!25;UBERON:0002619!2.83e-17!22;UBERON:0000033!3.49e-17!123;UBERON:0000153!4.24e-17!129;UBERON:0007811!4.24e-17!129;UBERON:0001950!5.61e-16!20;UBERON:0000475!3.85e-13!365;UBERON:0002420!2.65e-07!9;UBERON:0007245!2.65e-07!9;UBERON:0010009!2.65e-07!9;UBERON:0010011!2.65e-07!9;UBERON:0000454!2.65e-07!9;UBERON:0002308!3.26e-07!9;UBERON:0000125!3.26e-07!9;UBERON:0003076!5.82e-07!15;UBERON:0003057!5.82e-07!15;UBERON:0000468!6.15e-07!659
|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370215319450432!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279601961146333
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}}
}}

Revision as of 12:33, 5 September 2012


Full id: C2174_parietal_occipital_Saos2_caudate_lung_small_putamen



Phase1 CAGE Peaks

Hg19::chr11:91957816..91957827,+p@chr11:91957816..91957827
+
Hg19::chr11:91957916..91957921,+p@chr11:91957916..91957921
+
Hg19::chr11:91957974..91957992,+p@chr11:91957974..91957992
+
Hg19::chr11:92145586..92145591,+p@chr11:92145586..92145591
+


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell3.98e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.36e-4094
nervous system1.36e-4094
central nervous system7.44e-3982
neural tube8.35e-3457
neural rod8.35e-3457
future spinal cord8.35e-3457
neural keel8.35e-3457
regional part of brain1.88e-3059
brain2.10e-3069
future brain2.10e-3069
regional part of forebrain2.60e-2841
forebrain2.60e-2841
future forebrain2.60e-2841
anterior neural tube2.80e-2842
neural plate4.25e-2886
presumptive neural plate4.25e-2886
neurectoderm7.27e-2890
gray matter4.62e-2534
brain grey matter4.62e-2534
telencephalon4.88e-2534
pre-chordal neural plate2.62e-2461
regional part of telencephalon2.81e-2433
cerebral hemisphere3.01e-2432
adult organism8.41e-23115
ectoderm9.01e-21173
presumptive ectoderm9.01e-21173
ectoderm-derived structure1.40e-20169
cerebral cortex2.75e-1925
pallium2.75e-1925
regional part of cerebral cortex2.83e-1722
head3.49e-17123
anterior region of body4.24e-17129
craniocervical region4.24e-17129
neocortex5.61e-1620
organism subdivision3.85e-13365
basal ganglion2.65e-079
nuclear complex of neuraxis2.65e-079
aggregate regional part of brain2.65e-079
collection of basal ganglia2.65e-079
cerebral subcortex2.65e-079
nucleus of brain3.26e-079
neural nucleus3.26e-079
posterior neural tube5.82e-0715
chordal neural plate5.82e-0715
multi-cellular organism6.15e-07659


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
CTBP2#1488347.03775025449611.60047699357395e-050.000370215319450432
ZNF263#1012736.166381227758010.006539814347975980.0279601961146333



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:C2174&oldid=2131315"