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Coexpression cluster:C3703: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3703_acute_medial_parietal_heart_pineal_cerebellum_occipital
|full_id=C3703_acute_medial_parietal_heart_pineal_cerebellum_occipital
|id=C3703
|id=C3703

Revision as of 16:40, 12 September 2012


Full id: C3703_acute_medial_parietal_heart_pineal_cerebellum_occipital



Phase1 CAGE Peaks

Hg19::chr17:80708343..80708408,+p@chr17:80708343..80708408
+
Hg19::chr17:80708453..80708483,+p@chr17:80708453..80708483
+
Hg19::chr17:80708511..80708535,+p@chr17:80708511..80708535
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism5.06e-33115
neural tube1.96e-2857
neural rod1.96e-2857
future spinal cord1.96e-2857
neural keel1.96e-2857
regional part of nervous system2.74e-2894
nervous system2.74e-2894
central nervous system5.13e-2782
brain5.67e-2569
future brain5.67e-2569
neurectoderm2.06e-2490
regional part of brain1.25e-2359
neural plate2.99e-2386
presumptive neural plate2.99e-2386
regional part of forebrain2.45e-2241
forebrain2.45e-2241
future forebrain2.45e-2241
anterior neural tube5.32e-2242
ectoderm3.03e-19173
presumptive ectoderm3.03e-19173
gray matter1.40e-1834
brain grey matter1.40e-1834
telencephalon2.01e-1834
ectoderm-derived structure3.48e-18169
regional part of telencephalon6.72e-1833
pre-chordal neural plate1.25e-1761
head1.62e-17123
cerebral hemisphere3.03e-1732
anterior region of body7.99e-16129
craniocervical region7.99e-16129
multi-tissue structure1.08e-15347
anatomical conduit3.04e-15241
regional part of cerebral cortex3.33e-1422
anatomical cluster1.15e-13286
cerebral cortex2.89e-1325
pallium2.89e-1325
tube3.17e-13194
organism subdivision4.79e-13365
neocortex5.95e-1320
epithelium9.48e-11309
multi-cellular organism1.03e-10659
cell layer2.03e-10312
organ part3.69e-08219
organ3.94e-08511
embryo4.35e-08612
posterior neural tube1.34e-0715
chordal neural plate1.34e-0715
subdivision of digestive tract4.49e-07129
endodermal part of digestive tract4.49e-07129
basal ganglion6.70e-079
nuclear complex of neuraxis6.70e-079
aggregate regional part of brain6.70e-079
collection of basal ganglia6.70e-079
cerebral subcortex6.70e-079
anatomical system7.22e-07625
embryonic structure7.48e-07605
developing anatomical structure7.48e-07605
nucleus of brain7.54e-079
neural nucleus7.54e-079
germ layer8.30e-07604
embryonic tissue8.30e-07604
presumptive structure8.30e-07604
epiblast (generic)8.30e-07604
Disease
Ontology termp-valuen
cell type cancer3.60e-08143


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
SETDB1#9869340.32002617801051.52461559299059e-050.000358543859302734



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.

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