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Coexpression cluster:C4395: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!6.33e-110!56;UBERON:0005068!6.33e-110!56;UBERON:0006241!6.33e-110!56;UBERON:0007135!6.33e-110!56;UBERON:0000073!2.25e-98!53;UBERON:0002616!2.25e-98!53;UBERON:0001017!4.39e-86!81;UBERON:0002780!5.70e-82!41;UBERON:0001890!5.70e-82!41;UBERON:0003080!5.70e-82!41;UBERON:0006240!5.70e-82!41;UBERON:0000955!6.04e-79!68;UBERON:0006238!6.04e-79!68;UBERON:0001016!6.74e-77!89;UBERON:0003075!4.24e-73!82;UBERON:0007284!4.24e-73!82;UBERON:0001893!1.26e-72!34;UBERON:0003528!1.92e-72!34;UBERON:0002020!1.92e-72!34;UBERON:0001869!4.26e-71!32;UBERON:0002346!2.19e-69!86;UBERON:0002791!7.80e-65!32;UBERON:0002619!3.93e-63!22;UBERON:0010371!3.61e-56!104;UBERON:0000956!2.39e-55!25;UBERON:0000203!2.39e-55!25;UBERON:0001950!1.30e-54!20;UBERON:0003056!1.96e-53!61;UBERON:0007023!3.12e-51!114;UBERON:0010314!2.40e-45!132;UBERON:0004121!6.35e-37!171;UBERON:0000924!6.35e-37!171;UBERON:0006601!6.35e-37!171;UBERON:0011216!4.24e-28!223;UBERON:0003076!2.24e-27!15;UBERON:0003057!2.24e-27!15;UBERON:0000025!5.36e-27!192;UBERON:0001871!2.47e-24!6;UBERON:0000349!3.02e-24!5;UBERON:0000200!4.77e-20!6;UBERON:0004111!4.79e-20!240;UBERON:0002420!7.35e-19!9;UBERON:0007245!7.35e-19!9;UBERON:0010009!7.35e-19!9;UBERON:0010011!7.35e-19!9;UBERON:0000454!7.35e-19!9;UBERON:0002298!3.26e-18!6;UBERON:0000125!4.33e-18!9;UBERON:0002308!4.33e-18!9;UBERON:0004733!4.76e-17!12;UBERON:0002028!4.76e-17!12;UBERON:0007277!4.76e-17!12;UBERON:0004732!1.14e-15!13;UBERON:0001872!1.77e-15!5;UBERON:0000483!5.02e-14!306;UBERON:0002240!7.24e-14!3;UBERON:0005174!7.24e-14!3;UBERON:0001137!7.24e-14!3;UBERON:0000119!8.20e-14!309;UBERON:0000988!1.08e-13!3;UBERON:0000477!1.23e-13!373;UBERON:0000064!1.90e-12!218;UBERON:0002680!6.08e-12!9;UBERON:0001895!6.08e-12!9;UBERON:0010092!6.08e-12!9;UBERON:0000369!1.28e-11!4;UBERON:0002435!1.28e-11!4;UBERON:0000204!1.28e-11!4;UBERON:0010082!1.28e-11!4;UBERON:0009663!4.30e-11!7;UBERON:0001876!5.03e-11!2;UBERON:0002771!7.77e-11!2;UBERON:0001894!9.34e-11!7;UBERON:0006222!9.34e-11!7;UBERON:0000007!1.25e-10!2;UBERON:0001954!1.38e-10!2;UBERON:0003022!1.38e-10!2;UBERON:0002421!1.38e-10!2;UBERON:0002600!1.38e-10!2;UBERON:0000481!6.24e-10!342;UBERON:0002148!7.68e-10!2;UBERON:0006331!7.68e-10!2;UBERON:0009662!7.68e-10!2;UBERON:0002021!5.38e-09!5;UBERON:0005383!1.47e-07!3;UBERON:0005382!1.47e-07!3;UBERON:0001870!1.62e-07!3;UBERON:0000062!3.02e-07!503;UBERON:0001896!6.72e-07!3;UBERON:0005290!6.72e-07!3;UBERON:0010096!6.72e-07!3
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}}
}}

Revision as of 16:43, 26 November 2012


Full id: C4395_putamen_pituitary_frontal_caudate_amygdala_nucleus_cerebral



Phase1 CAGE Peaks

Hg19::chr4:175750301..175750313,-p2@GLRA3
Hg19::chr4:176828294..176828305,-p31@GPM6A
Hg19::chr5:156772645..156772690,-p1@FNDC9


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:0016934extracellular-glycine-gated chloride channel activity0.00824159647213382
GO:0016933extracellular-glycine-gated ion channel activity0.00824159647213382
GO:0004890GABA-A receptor activity0.0283886005769037
GO:0016917GABA receptor activity0.0283886005769037
GO:0043168anion binding0.0283886005769037
GO:0031404chloride ion binding0.0283886005769037
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0283886005769037
GO:0044459plasma membrane part0.0283886005769037
GO:0005254chloride channel activity0.0283886005769037
GO:0006821chloride transport0.0283886005769037
GO:0005253anion channel activity0.0283886005769037
GO:0005230extracellular ligand-gated ion channel activity0.0283886005769037
GO:0030594neurotransmitter receptor activity0.0283886005769037
GO:0042165neurotransmitter binding0.0283886005769037
GO:0009986cell surface0.0283886005769037
GO:0045211postsynaptic membrane0.0283886005769037
GO:0044456synapse part0.0283886005769037
GO:0015276ligand-gated ion channel activity0.0283886005769037
GO:0022834ligand-gated channel activity0.0283886005769037
GO:0008509anion transmembrane transporter activity0.0336389316043571
GO:0005886plasma membrane0.0336389316043571
GO:0015698inorganic anion transport0.0388140398722077
GO:0007268synaptic transmission0.0413919419054682
GO:0006820anion transport0.0433074604608263
GO:0019226transmission of nerve impulse0.0433074604608263



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 tube6.33e-11056
neural rod6.33e-11056
future spinal cord6.33e-11056
neural keel6.33e-11056
regional part of nervous system2.25e-9853
regional part of brain2.25e-9853
central nervous system4.39e-8681
regional part of forebrain5.70e-8241
forebrain5.70e-8241
anterior neural tube5.70e-8241
future forebrain5.70e-8241
brain6.04e-7968
future brain6.04e-7968
nervous system6.74e-7789
neural plate4.24e-7382
presumptive neural plate4.24e-7382
telencephalon1.26e-7234
brain grey matter1.92e-7234
gray matter1.92e-7234
cerebral hemisphere4.26e-7132
neurectoderm2.19e-6986
regional part of telencephalon7.80e-6532
regional part of cerebral cortex3.93e-6322
ecto-epithelium3.61e-56104
cerebral cortex2.39e-5525
pallium2.39e-5525
neocortex1.30e-5420
pre-chordal neural plate1.96e-5361
adult organism3.12e-51114
structure with developmental contribution from neural crest2.40e-45132
ectoderm-derived structure6.35e-37171
ectoderm6.35e-37171
presumptive ectoderm6.35e-37171
organ system subdivision4.24e-28223
posterior neural tube2.24e-2715
chordal neural plate2.24e-2715
tube5.36e-27192
temporal lobe2.47e-246
limbic system3.02e-245
gyrus4.77e-206
anatomical conduit4.79e-20240
basal ganglion7.35e-199
nuclear complex of neuraxis7.35e-199
aggregate regional part of brain7.35e-199
collection of basal ganglia7.35e-199
cerebral subcortex7.35e-199
brainstem3.26e-186
neural nucleus4.33e-189
nucleus of brain4.33e-189
segmental subdivision of hindbrain4.76e-1712
hindbrain4.76e-1712
presumptive hindbrain4.76e-1712
segmental subdivision of nervous system1.14e-1513
parietal lobe1.77e-155
epithelium5.02e-14306
spinal cord7.24e-143
dorsal region element7.24e-143
dorsum7.24e-143
cell layer8.20e-14309
pons1.08e-133
anatomical cluster1.23e-13373
organ part1.90e-12218
regional part of metencephalon6.08e-129
metencephalon6.08e-129
future metencephalon6.08e-129
corpus striatum1.28e-114
striatum1.28e-114
ventral part of telencephalon1.28e-114
future corpus striatum1.28e-114
telencephalic nucleus4.30e-117
amygdala5.03e-112
middle temporal gyrus7.77e-112
diencephalon9.34e-117
future diencephalon9.34e-117
pituitary gland1.25e-102
Ammon's horn1.38e-102
lobe parts of cerebral cortex1.38e-102
hippocampal formation1.38e-102
limbic lobe1.38e-102
multi-tissue structure6.24e-10342
locus ceruleus7.68e-102
brainstem nucleus7.68e-102
hindbrain nucleus7.68e-102
occipital lobe5.38e-095
caudate-putamen1.47e-073
dorsal striatum1.47e-073
frontal cortex1.62e-073
organ3.02e-07503
medulla oblongata6.72e-073
myelencephalon6.72e-073
future myelencephalon6.72e-073


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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