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Coexpression cluster:C3825: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.19e-34!115;UBERON:0000073!1.12e-30!94;UBERON:0001016!1.12e-30!94;UBERON:0001049!6.10e-30!57;UBERON:0005068!6.10e-30!57;UBERON:0006241!6.10e-30!57;UBERON:0007135!6.10e-30!57;UBERON:0001017!6.53e-30!82;UBERON:0005743!3.76e-29!86;UBERON:0000955!2.55e-28!69;UBERON:0006238!2.55e-28!69;UBERON:0002616!2.86e-27!59;UBERON:0002346!3.12e-26!90;UBERON:0000924!2.39e-25!173;UBERON:0006601!2.39e-25!173;UBERON:0003075!4.79e-25!86;UBERON:0007284!4.79e-25!86;UBERON:0003080!1.26e-24!42;UBERON:0002780!1.70e-24!41;UBERON:0001890!1.70e-24!41;UBERON:0006240!1.70e-24!41;UBERON:0004121!3.66e-24!169;UBERON:0000153!9.45e-23!129;UBERON:0007811!9.45e-23!129;UBERON:0000033!1.49e-22!123;UBERON:0002020!2.29e-20!34;UBERON:0003528!2.29e-20!34;UBERON:0001893!3.12e-20!34;UBERON:0002791!1.06e-19!33;UBERON:0001869!5.34e-19!32;UBERON:0003056!5.19e-18!61;UBERON:0000956!9.46e-15!25;UBERON:0000203!9.46e-15!25;UBERON:0002619!1.70e-14!22;UBERON:0001950!2.95e-13!20;UBERON:0000475!9.04e-13!365;UBERON:0000468!2.46e-09!659;UBERON:0000062!3.39e-09!511;UBERON:0000481!1.80e-08!347;UBERON:0000467!1.48e-07!625;UBERON:0000480!2.50e-07!626;UBERON:0002308!4.08e-07!9;UBERON:0000125!4.08e-07!9;UBERON:0002420!4.39e-07!9;UBERON:0007245!4.39e-07!9;UBERON:0010009!4.39e-07!9;UBERON:0010011!4.39e-07!9;UBERON:0000454!4.39e-07!9
|ontology_enrichment_uberon=UBERON:0007023!5.19e-34!115;UBERON:0000073!1.12e-30!94;UBERON:0001016!1.12e-30!94;UBERON:0001049!6.10e-30!57;UBERON:0005068!6.10e-30!57;UBERON:0006241!6.10e-30!57;UBERON:0007135!6.10e-30!57;UBERON:0001017!6.53e-30!82;UBERON:0005743!3.76e-29!86;UBERON:0000955!2.55e-28!69;UBERON:0006238!2.55e-28!69;UBERON:0002616!2.86e-27!59;UBERON:0002346!3.12e-26!90;UBERON:0000924!2.39e-25!173;UBERON:0006601!2.39e-25!173;UBERON:0003075!4.79e-25!86;UBERON:0007284!4.79e-25!86;UBERON:0003080!1.26e-24!42;UBERON:0002780!1.70e-24!41;UBERON:0001890!1.70e-24!41;UBERON:0006240!1.70e-24!41;UBERON:0004121!3.66e-24!169;UBERON:0000153!9.45e-23!129;UBERON:0007811!9.45e-23!129;UBERON:0000033!1.49e-22!123;UBERON:0002020!2.29e-20!34;UBERON:0003528!2.29e-20!34;UBERON:0001893!3.12e-20!34;UBERON:0002791!1.06e-19!33;UBERON:0001869!5.34e-19!32;UBERON:0003056!5.19e-18!61;UBERON:0000956!9.46e-15!25;UBERON:0000203!9.46e-15!25;UBERON:0002619!1.70e-14!22;UBERON:0001950!2.95e-13!20;UBERON:0000475!9.04e-13!365;UBERON:0000468!2.46e-09!659;UBERON:0000062!3.39e-09!511;UBERON:0000481!1.80e-08!347;UBERON:0000467!1.48e-07!625;UBERON:0000480!2.50e-07!626;UBERON:0002308!4.08e-07!9;UBERON:0000125!4.08e-07!9;UBERON:0002420!4.39e-07!9;UBERON:0007245!4.39e-07!9;UBERON:0010009!4.39e-07!9;UBERON:0010011!4.39e-07!9;UBERON:0000454!4.39e-07!9
|tf_chipseq_enrich=NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174459790746112!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239750377316882
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}}
}}

Revision as of 11:53, 5 September 2012


Full id: C3825_cerebellum_thalamus_middle_parietal_duodenum_globus_occipital



Phase1 CAGE Peaks

Hg19::chr19:57019215..57019250,+p1@ZNF471
Hg19::chr19:57019423..57019505,+p@chr19:57019423..57019505
+
Hg19::chr2:24150121..24150174,+p2@UBXN2A


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 organism5.19e-34115
regional part of nervous system1.12e-3094
nervous system1.12e-3094
neural tube6.10e-3057
neural rod6.10e-3057
future spinal cord6.10e-3057
neural keel6.10e-3057
central nervous system6.53e-3082
brain2.55e-2869
future brain2.55e-2869
regional part of brain2.86e-2759
neurectoderm3.12e-2690
ectoderm2.39e-25173
presumptive ectoderm2.39e-25173
neural plate4.79e-2586
presumptive neural plate4.79e-2586
anterior neural tube1.26e-2442
regional part of forebrain1.70e-2441
forebrain1.70e-2441
future forebrain1.70e-2441
ectoderm-derived structure3.66e-24169
anterior region of body9.45e-23129
craniocervical region9.45e-23129
head1.49e-22123
gray matter2.29e-2034
brain grey matter2.29e-2034
telencephalon3.12e-2034
regional part of telencephalon1.06e-1933
cerebral hemisphere5.34e-1932
pre-chordal neural plate5.19e-1861
cerebral cortex9.46e-1525
pallium9.46e-1525
regional part of cerebral cortex1.70e-1422
neocortex2.95e-1320
organism subdivision9.04e-13365
multi-cellular organism2.46e-09659
organ3.39e-09511
multi-tissue structure1.80e-08347
anatomical system1.48e-07625
anatomical group2.50e-07626
nucleus of brain4.08e-079
neural nucleus4.08e-079
basal ganglion4.39e-079
nuclear complex of neuraxis4.39e-079
aggregate regional part of brain4.39e-079
collection of basal ganglia4.39e-079
cerebral subcortex4.39e-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
NANOG#79923219.49651898734180.003427255648501020.0174459790746112
SIX5#147912317.0867153554590.0002004060546325010.00239750377316882



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:C3825&oldid=2130679"