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Coexpression cluster:C2110: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:00, 8 August 2012


Full id: C2110_amygdala_occipital_medial_parietal_putamen_temporal_brain



Phase1 CAGE Peaks

Hg19::chr11:128842905..128842917,-p13@ARHGAP32
Hg19::chr13:66878762..66878772,-p@chr13:66878762..66878772
-
Hg19::chr19:5681211..5681216,+p6@HSD11B1L
Hg19::chr6:24146395..24146398,+p@chr6:24146395..24146398
+


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:0016491oxidoreductase activity0.0458024255269045



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
neural tube3.03e-3157
neural rod3.03e-3157
future spinal cord3.03e-3157
neural keel3.03e-3157
central nervous system9.41e-2982
brain1.29e-2869
future brain1.29e-2869
regional part of brain1.98e-2759
regional part of forebrain8.75e-2741
forebrain8.75e-2741
future forebrain8.75e-2741
anterior neural tube8.85e-2642
regional part of nervous system1.13e-2594
nervous system1.13e-2594
gray matter7.70e-2534
brain grey matter7.70e-2534
telencephalon1.16e-2434
regional part of telencephalon1.12e-2333
cerebral hemisphere4.22e-2332
neural plate2.16e-2186
presumptive neural plate2.16e-2186
neurectoderm3.66e-2190
regional part of cerebral cortex4.18e-2122
adult organism3.07e-19115
neocortex3.46e-1920
cerebral cortex7.94e-1925
pallium7.94e-1925
pre-chordal neural plate1.51e-1861
ectoderm4.96e-15173
presumptive ectoderm4.96e-15173
ectoderm-derived structure6.41e-15169
anterior region of body6.95e-15129
craniocervical region6.95e-15129
head3.86e-14123
organism subdivision4.74e-08365
basal ganglion1.46e-079
nuclear complex of neuraxis1.46e-079
aggregate regional part of brain1.46e-079
collection of basal ganglia1.46e-079
cerebral subcortex1.46e-079
gyrus1.52e-076
nucleus of brain1.90e-079
neural nucleus1.90e-079
tube2.93e-07194
temporal lobe3.12e-077
posterior neural tube7.93e-0715
chordal neural plate7.93e-0715


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.

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