Personal tools

Coexpression cluster:C460


Revision as of 07:05, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C460_Neutrophils_corpus_thalamus_substantia_parietal_globus_locus

Phase1 CAGE Peaks

  Short description
Hg19::chr10:1278750..1278767,- p@chr10:1278750..1278767
Hg19::chr10:1282470..1282519,- p3@ADARB2
Hg19::chr11:78049190..78049232,- p@chr11:78049190..78049232
Hg19::chr2:71804278..71804331,+ +
Hg19::chr4:185729602..185729613,- p15@ACSL1
Hg19::chr9:91985133..91985173,- p@chr9:91985133..91985173
Hg19::chr9:91985218..91985232,- p@chr9:91985218..91985232
Hg19::chr9:91985236..91985347,- p@chr9:91985236..91985347
Hg19::chr9:91985398..91985439,- p@chr9:91985398..91985439
Hg19::chr9:91985441..91985477,- p@chr9:91985441..91985477
Hg19::chr9:91985535..91985584,- p@chr9:91985535..91985584
Hg19::chr9:91985611..91985646,- p@chr9:91985611..91985646
Hg19::chr9:91985687..91985700,- p@chr9:91985687..91985700
Hg19::chr9:91985741..91985765,- p@chr9:91985741..91985765
Hg19::chr9:91985867..91985882,- p@chr9:91985867..91985882
Hg19::chr9:91985883..91985947,- p@chr9:91985883..91985947
Hg19::chr9:91986315..91986327,- p@chr9:91986315..91986327
Hg19::chr9:91987177..91987203,- p@chr9:91987177..91987203
Hg19::chr9:91987221..91987232,- p@chr9:91987221..91987232
Hg19::chr9:91987337..91987359,- p@chr9:91987337..91987359
Hg19::chr9:91987399..91987413,- p@chr9:91987399..91987413

Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset

GO IDGO nameFDR corrected p-value
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0202658856665421
GO:0015645fatty-acid ligase activity0.0202658856665421
GO:0004000adenosine deaminase activity0.0202658856665421
GO:0003727single-stranded RNA binding0.0202658856665421
GO:0016877ligase activity, forming carbon-sulfur bonds0.0202658856665421
GO:0019239deaminase activity0.0202658856665421
GO:0031903microbody membrane0.0202658856665421
GO:0005778peroxisomal membrane0.0202658856665421
GO:0044439peroxisomal part0.0202658856665421
GO:0044438microbody part0.0202658856665421
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0202658856665421
GO:0003725double-stranded RNA binding0.0202658856665421
GO:0005741mitochondrial outer membrane0.0254740322863236
GO:0031968organelle outer membrane0.0254740322863236
GO:0019867outer membrane0.0254740322863236
GO:0042598vesicular fraction0.0387065963269252
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0397555679538304
GO:0006631fatty acid metabolic process0.0397555679538304

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


Uber Anatomy
Ontology termp-valuen
neural tube1.05e-4356
neural rod1.05e-4356
future spinal cord1.05e-4356
neural keel1.05e-4356
regional part of nervous system2.74e-4053
regional part of brain2.74e-4053
adult organism7.31e-36114
regional part of forebrain1.09e-3541
anterior neural tube1.09e-3541
future forebrain1.09e-3541
future brain7.83e-3468
central nervous system7.68e-3381
nervous system2.27e-3189
neural plate3.19e-2982
presumptive neural plate3.19e-2982
brain grey matter3.19e-2834
gray matter3.19e-2834
regional part of telencephalon7.04e-2632
cerebral hemisphere1.11e-2532
pre-chordal neural plate1.79e-2361
regional part of cerebral cortex1.30e-2122
cerebral cortex3.34e-1825
structure with developmental contribution from neural crest5.59e-15132
basal ganglion5.87e-129
nuclear complex of neuraxis5.87e-129
aggregate regional part of brain5.87e-129
collection of basal ganglia5.87e-129
cerebral subcortex5.87e-129
neural nucleus6.49e-129
nucleus of brain6.49e-129
ectoderm-derived structure2.56e-10171
presumptive ectoderm2.56e-10171
telencephalic nucleus1.55e-097
posterior neural tube2.89e-0915
chordal neural plate2.89e-0915
future diencephalon5.38e-097
organ system subdivision1.43e-08223
limbic system2.03e-075
segmental subdivision of nervous system2.53e-0713
parietal lobe4.60e-075
temporal lobe9.55e-076

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs

Jaspar motifs

Novel motifs

JASPAR motifs



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)


Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.

link to data source

This analysis result is provided for C0 - C305 clusters.