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Coexpression cluster:C1166

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Full id: C1166_cerebellum_occipital_middle_pineal_parietal_thalamus_acute



Phase1 CAGE Peaks

Hg19::chr12:132640129..132640150,+p@chr12:132640129..132640150
+
Hg19::chr1:7552597..7552608,+p@chr1:7552597..7552608
+
Hg19::chr3:129089024..129089057,-p@chr3:129089024..129089057
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Hg19::chr3:129089229..129089276,-p@chr3:129089229..129089276
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Hg19::chr3:129089385..129089423,-p@chr3:129089385..129089423
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Hg19::chr3:129089547..129089586,-p@chr3:129089547..129089586
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Hg19::chr3:129089810..129089831,-p@chr3:129089810..129089831
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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
neural tube1.88e-2856
neural rod1.88e-2856
future spinal cord1.88e-2856
neural keel1.88e-2856
regional part of nervous system7.96e-2853
regional part of brain7.96e-2853
brain8.77e-2668
future brain8.77e-2668
central nervous system1.07e-2481
regional part of forebrain4.65e-2441
forebrain4.65e-2441
anterior neural tube4.65e-2441
future forebrain4.65e-2441
nervous system8.10e-2489
adult organism4.05e-22114
brain grey matter3.58e-2034
gray matter3.58e-2034
telencephalon5.20e-2034
neurectoderm8.00e-1986
regional part of telencephalon1.18e-1832
cerebral hemisphere1.95e-1832
neural plate3.01e-1782
presumptive neural plate3.01e-1782
regional part of cerebral cortex1.08e-1522
neocortex4.63e-1420
cerebral cortex8.72e-1425
pallium8.72e-1425
pre-chordal neural plate1.11e-1361
organ system subdivision1.79e-11223
ecto-epithelium2.16e-11104
ectoderm-derived structure1.14e-09171
ectoderm1.14e-09171
presumptive ectoderm1.14e-09171
neural nucleus5.00e-089
nucleus of brain5.00e-089
structure with developmental contribution from neural crest5.86e-08132
basal ganglion6.87e-089
nuclear complex of neuraxis6.87e-089
aggregate regional part of brain6.87e-089
collection of basal ganglia6.87e-089
cerebral subcortex6.87e-089
Disease
Ontology termp-valuen
cell type cancer7.10e-09143
cancer1.96e-08235
disease of cellular proliferation6.93e-08239


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
NR2C2#7182418.63692051728052.86862168958321e-050.000604145958133457
SUZ12#23512428.63758909203595.27895839013948e-060.000161348883613631



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.