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Coexpression cluster:C3337

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Full id: C3337_kidney_umbilical_retina_putamen_Ciliary_brain_caudate



Phase1 CAGE Peaks

Hg19::chr12:80794469..80794483,+p@chr12:80794469..80794483
+
Hg19::chr12:80794499..80794508,+p@chr12:80794499..80794508
+
Hg19::chr3:64547432..64547444,-p@chr3:64547432..64547444
-


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
ciliated cell1.43e-083
multi-ciliated epithelial cell1.43e-083
ciliated epithelial cell1.43e-083
non-pigmented ciliary epithelial cell1.43e-083
Uber Anatomy
Ontology termp-valuen
adult organism3.20e-34115
regional part of brain1.33e-3259
neural tube8.47e-3257
neural rod8.47e-3257
future spinal cord8.47e-3257
neural keel8.47e-3257
brain3.14e-3069
future brain3.14e-3069
neural plate3.58e-3086
presumptive neural plate3.58e-3086
neurectoderm4.46e-3090
regional part of forebrain1.32e-2741
forebrain1.32e-2741
future forebrain1.32e-2741
anterior neural tube8.47e-2742
telencephalon5.88e-2634
pre-chordal neural plate6.60e-2661
central nervous system7.68e-2682
cerebral hemisphere2.56e-2532
head3.03e-24123
regional part of telencephalon3.58e-2433
anterior region of body6.31e-24129
craniocervical region6.31e-24129
regional part of cerebral cortex7.89e-2422
gray matter2.61e-2334
brain grey matter2.61e-2334
neocortex3.43e-2320
regional part of nervous system1.08e-2294
nervous system1.08e-2294
cerebral cortex1.45e-2025
pallium1.45e-2025
ectoderm8.59e-16173
presumptive ectoderm8.59e-16173
ectoderm-derived structure1.74e-15169
temporal lobe6.52e-117
gyrus2.40e-106
ciliary epithelium1.43e-083
ciliary body1.43e-083
limbic system2.11e-085
segmental subdivision of hindbrain2.29e-0812
hindbrain2.29e-0812
presumptive hindbrain2.29e-0812
parietal lobe3.03e-085
middle temporal gyrus3.46e-083
medulla oblongata1.09e-073
myelencephalon1.09e-073
future myelencephalon1.09e-073
segmental subdivision of nervous system1.21e-0713
organism subdivision3.03e-07365
tube3.17e-07194
basal ganglion3.49e-079
nuclear complex of neuraxis3.49e-079
aggregate regional part of brain3.49e-079
collection of basal ganglia3.49e-079
cerebral subcortex3.49e-079
organ part4.31e-07219
brainstem4.89e-078


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


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.