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Coexpression cluster:C1860: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0008503!benzodiazepine receptor activity!0.0230672990440317!2566$GO:0007026!negative regulation of microtubule depolymerization!0.0230672990440317!4133$GO:0031114!regulation of microtubule depolymerization!0.0230672990440317!4133$GO:0007019!microtubule depolymerization!0.0230672990440317!4133$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0007214!gamma-aminobutyric acid signaling pathway!0.0230672990440317!2566$GO:0031110!regulation of microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0031109!microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0004890!GABA-A receptor activity!0.0246346270007797!2566$GO:0051261!protein depolymerization!0.0246346270007797!4133$GO:0016917!GABA receptor activity!0.0246346270007797!2566$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0247047731748591!4133$GO:0043168!anion binding!0.0247047731748591!2566$GO:0031404!chloride ion binding!0.0247047731748591!2566$GO:0005254!chloride channel activity!0.0299556956870386!2566$GO:0006821!chloride transport!0.0299556956870386!2566$GO:0051128!regulation of cellular component organization and biogenesis!0.0299556956870386!4133$GO:0005253!anion channel activity!0.0299556956870386!2566$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0299556956870386!4133$GO:0051248!negative regulation of protein metabolic process!0.0299556956870386!4133$GO:0005230!extracellular ligand-gated ion channel activity!0.0337114631850732!2566$GO:0005516!calmodulin binding!0.0337114631850732!4133$GO:0030594!neurotransmitter receptor activity!0.0337114631850732!2566$GO:0042165!neurotransmitter binding!0.0337114631850732!2566$GO:0045211!postsynaptic membrane!0.0337114631850732!2566$GO:0044456!synapse part!0.0337114631850732!2566$GO:0015276!ligand-gated ion channel activity!0.0337114631850732!2566$GO:0022834!ligand-gated channel activity!0.0337114631850732!2566$GO:0005875!microtubule associated complex!0.0357160778536372!4133$GO:0008509!anion transmembrane transporter activity!0.0400708342034334!2566$GO:0015698!inorganic anion transport!0.0482045333896773!2566
|gostat_on_coexpression_clusters=GO:0008503!benzodiazepine receptor activity!0.0230672990440317!2566$GO:0007026!negative regulation of microtubule depolymerization!0.0230672990440317!4133$GO:0031114!regulation of microtubule depolymerization!0.0230672990440317!4133$GO:0007019!microtubule depolymerization!0.0230672990440317!4133$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0007214!gamma-aminobutyric acid signaling pathway!0.0230672990440317!2566$GO:0031110!regulation of microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0031109!microtubule polymerization or depolymerization!0.0230672990440317!4133$GO:0004890!GABA-A receptor activity!0.0246346270007797!2566$GO:0051261!protein depolymerization!0.0246346270007797!4133$GO:0016917!GABA receptor activity!0.0246346270007797!2566$GO:0051129!negative regulation of cellular component organization and biogenesis!0.0247047731748591!4133$GO:0043168!anion binding!0.0247047731748591!2566$GO:0031404!chloride ion binding!0.0247047731748591!2566$GO:0005254!chloride channel activity!0.0299556956870386!2566$GO:0006821!chloride transport!0.0299556956870386!2566$GO:0051128!regulation of cellular component organization and biogenesis!0.0299556956870386!4133$GO:0005253!anion channel activity!0.0299556956870386!2566$GO:0000226!microtubule cytoskeleton organization and biogenesis!0.0299556956870386!4133$GO:0051248!negative regulation of protein metabolic process!0.0299556956870386!4133$GO:0005230!extracellular ligand-gated ion channel activity!0.0337114631850732!2566$GO:0005516!calmodulin binding!0.0337114631850732!4133$GO:0030594!neurotransmitter receptor activity!0.0337114631850732!2566$GO:0042165!neurotransmitter binding!0.0337114631850732!2566$GO:0045211!postsynaptic membrane!0.0337114631850732!2566$GO:0044456!synapse part!0.0337114631850732!2566$GO:0015276!ligand-gated ion channel activity!0.0337114631850732!2566$GO:0022834!ligand-gated channel activity!0.0337114631850732!2566$GO:0005875!microtubule associated complex!0.0357160778536372!4133$GO:0008509!anion transmembrane transporter activity!0.0400708342034334!2566$GO:0015698!inorganic anion transport!0.0482045333896773!2566
|id=C1860
|id=C1860
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000047!3.27e-08!8
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!5.55e-56!57;UBERON:0005068!5.55e-56!57;UBERON:0006241!5.55e-56!57;UBERON:0007135!5.55e-56!57;UBERON:0000073!5.67e-53!94;UBERON:0001016!5.67e-53!94;UBERON:0001017!1.62e-52!82;UBERON:0005743!9.95e-51!86;UBERON:0002346!1.00e-46!90;UBERON:0002616!1.37e-46!59;UBERON:0002780!1.46e-46!41;UBERON:0001890!1.46e-46!41;UBERON:0006240!1.46e-46!41;UBERON:0007023!1.60e-46!115;UBERON:0003075!1.62e-45!86;UBERON:0007284!1.62e-45!86;UBERON:0000955!3.14e-45!69;UBERON:0006238!3.14e-45!69;UBERON:0003080!4.72e-45!42;UBERON:0002020!8.55e-39!34;UBERON:0003528!8.55e-39!34;UBERON:0001893!1.28e-38!34;UBERON:0002791!1.65e-37!33;UBERON:0001869!8.17e-37!32;UBERON:0000924!1.36e-35!173;UBERON:0006601!1.36e-35!173;UBERON:0003056!2.04e-34!61;UBERON:0004121!3.20e-34!169;UBERON:0000153!9.73e-31!129;UBERON:0007811!9.73e-31!129;UBERON:0000033!2.24e-29!123;UBERON:0000956!6.04e-29!25;UBERON:0000203!6.04e-29!25;UBERON:0002619!4.57e-27!22;UBERON:0001950!8.06e-25!20;UBERON:0000064!7.73e-13!219;UBERON:0003076!6.91e-12!15;UBERON:0003057!6.91e-12!15;UBERON:0002420!2.58e-11!9;UBERON:0007245!2.58e-11!9;UBERON:0010009!2.58e-11!9;UBERON:0010011!2.58e-11!9;UBERON:0000454!2.58e-11!9;UBERON:0002308!3.63e-11!9;UBERON:0000125!3.63e-11!9;UBERON:0000025!5.07e-11!194;UBERON:0000483!5.66e-11!309;UBERON:0000475!1.14e-10!365;UBERON:0000119!1.32e-10!312;UBERON:0004111!1.38e-10!241;UBERON:0001871!2.64e-10!7;UBERON:0000481!2.92e-10!347;UBERON:0004732!6.05e-10!13;UBERON:0000477!2.21e-09!286;UBERON:0001894!3.38e-09!7;UBERON:0006222!3.38e-09!7;UBERON:0004733!4.36e-09!12;UBERON:0002028!4.36e-09!12;UBERON:0007277!4.36e-09!12;UBERON:0009663!4.82e-09!7;UBERON:0000922!8.11e-09!612;UBERON:0000200!1.77e-08!6;UBERON:0000062!7.91e-08!511;UBERON:0002298!2.76e-07!8;UBERON:0000349!3.54e-07!5;UBERON:0002021!3.63e-07!5;UBERON:0000923!3.87e-07!604;UBERON:0005291!3.87e-07!604;UBERON:0006598!3.87e-07!604;UBERON:0002532!3.87e-07!604;UBERON:0001872!4.14e-07!5;UBERON:0002050!4.62e-07!605;UBERON:0005423!4.62e-07!605;UBERON:0000468!7.81e-07!659
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}}
}}

Revision as of 11:46, 19 October 2012


Full id: C1860_occipital_pineal_medial_parietal_amygdala_caudate_frontal



Phase1 CAGE Peaks

Hg19::chr1:92634472..92634492,+p1@KIAA1107
Hg19::chr1:92634493..92634508,+p2@KIAA1107
Hg19::chr2:210444345..210444394,+p3@MAP2
Hg19::chr5:161580386..161580395,+p18@GABRG2
Hg19::chrX:38547830..38547849,+p@chrX:38547830..38547849
+


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:0008503benzodiazepine receptor activity0.0230672990440317
GO:0007026negative regulation of microtubule depolymerization0.0230672990440317
GO:0031114regulation of microtubule depolymerization0.0230672990440317
GO:0007019microtubule depolymerization0.0230672990440317
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0230672990440317
GO:0007214gamma-aminobutyric acid signaling pathway0.0230672990440317
GO:0031110regulation of microtubule polymerization or depolymerization0.0230672990440317
GO:0031109microtubule polymerization or depolymerization0.0230672990440317
GO:0004890GABA-A receptor activity0.0246346270007797
GO:0051261protein depolymerization0.0246346270007797
GO:0016917GABA receptor activity0.0246346270007797
GO:0051129negative regulation of cellular component organization and biogenesis0.0247047731748591
GO:0043168anion binding0.0247047731748591
GO:0031404chloride ion binding0.0247047731748591
GO:0005254chloride channel activity0.0299556956870386
GO:0006821chloride transport0.0299556956870386
GO:0051128regulation of cellular component organization and biogenesis0.0299556956870386
GO:0005253anion channel activity0.0299556956870386
GO:0000226microtubule cytoskeleton organization and biogenesis0.0299556956870386
GO:0051248negative regulation of protein metabolic process0.0299556956870386
GO:0005230extracellular ligand-gated ion channel activity0.0337114631850732
GO:0005516calmodulin binding0.0337114631850732
GO:0030594neurotransmitter receptor activity0.0337114631850732
GO:0042165neurotransmitter binding0.0337114631850732
GO:0045211postsynaptic membrane0.0337114631850732
GO:0044456synapse part0.0337114631850732
GO:0015276ligand-gated ion channel activity0.0337114631850732
GO:0022834ligand-gated channel activity0.0337114631850732
GO:0005875microtubule associated complex0.0357160778536372
GO:0008509anion transmembrane transporter activity0.0400708342034334
GO:0015698inorganic anion transport0.0482045333896773



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
neuronal stem cell3.27e-088
Uber Anatomy
Ontology termp-valuen
neural tube3.50e-11556
neural rod3.50e-11556
future spinal cord3.50e-11556
neural keel3.50e-11556
central nervous system4.06e-11581
regional part of nervous system1.07e-10753
regional part of brain1.07e-10753
nervous system7.01e-10689
brain1.89e-9568
future brain1.89e-9568
regional part of forebrain8.11e-9141
forebrain8.11e-9141
anterior neural tube8.11e-9141
future forebrain8.11e-9141
neural plate4.09e-7882
presumptive neural plate4.09e-7882
neurectoderm6.59e-7486
brain grey matter2.23e-7234
gray matter2.23e-7234
telencephalon4.19e-7234
cerebral hemisphere1.10e-6732
regional part of telencephalon3.15e-6732
pre-chordal neural plate3.43e-6161
ecto-epithelium6.08e-59104
regional part of cerebral cortex1.13e-5622
adult organism9.28e-56114
neocortex1.58e-5120
ectoderm-derived structure6.97e-51171
ectoderm6.97e-51171
presumptive ectoderm6.97e-51171
cerebral cortex2.21e-4925
pallium2.21e-4925
structure with developmental contribution from neural crest7.25e-48132
organ system subdivision3.57e-40223
tube2.34e-27192
basal ganglion1.19e-249
nuclear complex of neuraxis1.19e-249
aggregate regional part of brain1.19e-249
collection of basal ganglia1.19e-249
cerebral subcortex1.19e-249
posterior neural tube2.93e-2415
chordal neural plate2.93e-2415
neural nucleus2.99e-249
nucleus of brain2.99e-249
diencephalon1.13e-197
future diencephalon1.13e-197
anatomical conduit2.77e-19240
telencephalic nucleus2.93e-197
anatomical cluster5.21e-19373
gyrus6.73e-186
segmental subdivision of hindbrain1.21e-1712
hindbrain1.21e-1712
presumptive hindbrain1.21e-1712
brainstem3.06e-166
segmental subdivision of nervous system3.83e-1613
temporal lobe7.80e-156
limbic system1.09e-145
occipital lobe1.22e-145
parietal lobe1.44e-145
epithelium3.97e-13306
organ part4.90e-13218
cell layer7.09e-13309
regional part of diencephalon1.47e-124
corpus striatum2.62e-124
striatum2.62e-124
ventral part of telencephalon2.62e-124
future corpus striatum2.62e-124
gland of diencephalon6.88e-124
neuroendocrine gland6.88e-124
regional part of metencephalon2.80e-119
metencephalon2.80e-119
future metencephalon2.80e-119
frontal cortex3.72e-103
caudate-putamen9.51e-103
dorsal striatum9.51e-103
multi-tissue structure9.60e-10342
pons2.12e-093
germ layer1.11e-08560
germ layer / neural crest1.11e-08560
embryonic tissue1.11e-08560
presumptive structure1.11e-08560
germ layer / neural crest derived structure1.11e-08560
epiblast (generic)1.11e-08560
spinal cord1.35e-083
dorsal region element1.35e-083
dorsum1.35e-083
medulla oblongata1.51e-083
myelencephalon1.51e-083
future myelencephalon1.51e-083
embryonic structure1.65e-08564
embryo5.61e-08592
developing anatomical structure8.37e-08581
organ1.05e-07503
pineal body1.96e-072
regional part of epithalamus1.96e-072
secretory circumventricular organ1.96e-072
circumventricular organ1.96e-072
epithalamus1.96e-072
middle frontal gyrus2.57e-072


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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