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Coexpression cluster:C1836: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1836_optic_cerebellum_globus_locus_occipital_spinal_pineal
|full_id=C1836_optic_cerebellum_globus_locus_occipital_spinal_pineal
|gostat_on_coexpression_clusters=GO:0019902!phosphatase binding!0.0211830064584042!9863$GO:0019717!synaptosome!0.0211830064584042!9863
|gostat_on_coexpression_clusters=GO:0019902!phosphatase binding!0.0211830064584042!9863$GO:0019717!synaptosome!0.0211830064584042!9863

Revision as of 14:27, 12 September 2012


Full id: C1836_optic_cerebellum_globus_locus_occipital_spinal_pineal



Phase1 CAGE Peaks

Hg19::chr1:151431223..151431293,-p@chr1:151431223..151431293
-
Hg19::chr5:137225034..137225081,-p2@ENST00000508281
Hg19::chr7:79082958..79083004,-p1@MAGI2
Hg19::chrX:72783026..72783049,+p2@CHIC1
Hg19::chrX:72783111..72783137,+p1@CHIC1


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:0019902phosphatase binding0.0211830064584042
GO:0019717synaptosome0.0211830064584042



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 organism6.38e-43115
neural tube8.80e-2857
neural rod8.80e-2857
future spinal cord8.80e-2857
neural keel8.80e-2857
regional part of brain6.17e-2659
brain5.71e-2569
future brain5.71e-2569
regional part of nervous system2.64e-2394
nervous system2.64e-2394
anterior neural tube7.23e-2342
regional part of forebrain9.60e-2341
forebrain9.60e-2341
future forebrain9.60e-2341
central nervous system1.48e-2282
neural plate5.75e-2186
presumptive neural plate5.75e-2186
neurectoderm1.47e-2090
gray matter2.20e-1834
brain grey matter2.20e-1834
telencephalon2.44e-1834
anterior region of body5.02e-18129
craniocervical region5.02e-18129
regional part of telencephalon9.50e-1833
head2.55e-17123
cerebral hemisphere4.28e-1732
pre-chordal neural plate2.36e-1561
regional part of cerebral cortex3.83e-1522
ectoderm-derived structure1.53e-14169
ectoderm1.55e-14173
presumptive ectoderm1.55e-14173
neocortex6.58e-1420
cerebral cortex8.28e-1325
pallium8.28e-1325
organism subdivision8.51e-10365
multi-tissue structure2.98e-07347
nucleus of brain3.64e-079
neural nucleus3.64e-079
basal ganglion3.67e-079
nuclear complex of neuraxis3.67e-079
aggregate regional part of brain3.67e-079
collection of basal ganglia3.67e-079
cerebral subcortex3.67e-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
NRF1#489937.326167668626540.004839689817117540.0226904455382447
TAF1#687253.343046285745290.002394600090870310.0135432491546845
YY1#752843.928936599883080.007193866269917620.0298462717738818
ZNF263#1012746.577473309608540.0009875103237900160.0070931630472012



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.