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Coexpression cluster:C2226: Difference between revisions

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}}
}}

Revision as of 15:22, 26 November 2012


Full id: C2226_putamen_diencephalon_nucleus_brain_temporal_insula_caudate



Phase1 CAGE Peaks

Hg19::chr12:58027138..58027159,-p8@B4GALNT1
Hg19::chr1:33359673..33359704,-p@chr1:33359673..33359704
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Hg19::chr1:33359734..33359745,-p@chr1:33359734..33359745
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Hg19::chr1:33360078..33360094,-p@chr1:33360078..33360094
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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><br>

Uber Anatomy
Ontology termp-valuen
brain7.39e-5768
future brain7.39e-5768
regional part of nervous system6.11e-5453
regional part of brain6.11e-5453
central nervous system1.35e-5281
neural tube1.03e-5056
neural rod1.03e-5056
future spinal cord1.03e-5056
neural keel1.03e-5056
telencephalon1.18e-4934
nervous system1.37e-4989
regional part of forebrain8.72e-4941
forebrain8.72e-4941
anterior neural tube8.72e-4941
future forebrain8.72e-4941
cerebral hemisphere2.77e-4832
regional part of telencephalon1.89e-4332
neurectoderm9.65e-4186
brain grey matter1.14e-4034
gray matter1.14e-4034
regional part of cerebral cortex1.71e-4022
neural plate2.41e-4082
presumptive neural plate2.41e-4082
pre-chordal neural plate7.87e-4061
cerebral cortex2.34e-3525
pallium2.34e-3525
neocortex4.13e-3420
ecto-epithelium1.81e-32104
ectoderm-derived structure2.47e-28171
ectoderm2.47e-28171
presumptive ectoderm2.47e-28171
adult organism2.62e-27114
structure with developmental contribution from neural crest1.22e-25132
gyrus9.59e-246
organ system subdivision2.42e-18223
temporal lobe5.69e-146
limbic system5.72e-135
frontal cortex1.09e-123
basal ganglion5.15e-119
nuclear complex of neuraxis5.15e-119
aggregate regional part of brain5.15e-119
collection of basal ganglia5.15e-119
cerebral subcortex5.15e-119
tube6.50e-11192
corpus striatum4.39e-104
striatum4.39e-104
ventral part of telencephalon4.39e-104
future corpus striatum4.39e-104
telencephalic nucleus1.75e-097
middle temporal gyrus6.47e-092
middle frontal gyrus7.00e-092
anatomical cluster8.96e-09373
Ammon's horn9.94e-092
lobe parts of cerebral cortex9.94e-092
hippocampal formation9.94e-092
limbic lobe9.94e-092
organ part1.02e-08218
anatomical conduit4.33e-08240
parietal lobe7.97e-085
neural nucleus2.26e-079
nucleus of brain2.26e-079
segmental subdivision of hindbrain2.70e-0712
hindbrain2.70e-0712
presumptive hindbrain2.70e-0712
epithelium2.78e-07306
cell layer3.87e-07309


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.

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