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Coexpression cluster:C2685: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001893!4.68e-77!34;UBERON:0003528!7.62e-77!34;UBERON:0002020!7.62e-77!34;UBERON:0001869!2.86e-76!32;UBERON:0002791!6.22e-76!32;UBERON:0002780!4.71e-73!41;UBERON:0001890!4.71e-73!41;UBERON:0003080!4.71e-73!41;UBERON:0006240!4.71e-73!41;UBERON:0002619!3.03e-72!22;UBERON:0001049!5.03e-72!56;UBERON:0005068!5.03e-72!56;UBERON:0006241!5.03e-72!56;UBERON:0007135!5.03e-72!56;UBERON:0000073!7.30e-72!53;UBERON:0002616!7.30e-72!53;UBERON:0001950!1.33e-64!20;UBERON:0001017!2.55e-63!81;UBERON:0000956!2.85e-63!25;UBERON:0000203!2.85e-63!25;UBERON:0001016!2.68e-59!89;UBERON:0000955!3.75e-57!68;UBERON:0006238!3.75e-57!68;UBERON:0003056!4.34e-47!61;UBERON:0003075!7.66e-47!82;UBERON:0007284!7.66e-47!82;UBERON:0002346!2.64e-44!86;UBERON:0010371!1.16e-37!104;UBERON:0007023!1.45e-33!114;UBERON:0010314!7.78e-32!132;UBERON:0004121!2.31e-30!171;UBERON:0000924!2.31e-30!171;UBERON:0006601!2.31e-30!171;UBERON:0011216!4.62e-28!223;UBERON:0000200!1.12e-23!6;UBERON:0002420!9.32e-21!9;UBERON:0007245!9.32e-21!9;UBERON:0010009!9.32e-21!9;UBERON:0010011!9.32e-21!9;UBERON:0000454!9.32e-21!9;UBERON:0002021!2.02e-20!5;UBERON:0000025!2.34e-20!192;UBERON:0001871!2.65e-20!6;UBERON:0000349!5.20e-20!5;UBERON:0000369!1.63e-16!4;UBERON:0002435!1.63e-16!4;UBERON:0000204!1.63e-16!4;UBERON:0010082!1.63e-16!4;UBERON:0004111!1.34e-15!240;UBERON:0000125!3.71e-15!9;UBERON:0002308!3.71e-15!9;UBERON:0000064!1.24e-14!218;UBERON:0009663!5.39e-14!7;UBERON:0000477!9.78e-14!373;UBERON:0005383!4.56e-13!3;UBERON:0005382!4.56e-13!3;UBERON:0001872!5.22e-13!5;UBERON:0001870!7.07e-13!3;UBERON:0000483!3.89e-11!306;UBERON:0000119!6.10e-11!309;UBERON:0000481!1.49e-10!342;UBERON:0001954!2.81e-09!2;UBERON:0003022!2.81e-09!2;UBERON:0002421!2.81e-09!2;UBERON:0002600!2.81e-09!2;UBERON:0001873!2.92e-09!2;UBERON:0010122!2.92e-09!2;UBERON:0002702!3.57e-09!2;UBERON:0002771!3.87e-09!2;UBERON:0001876!5.31e-09!2;UBERON:0000923!6.74e-07!560;UBERON:0010316!6.74e-07!560;UBERON:0005291!6.74e-07!560;UBERON:0006598!6.74e-07!560;UBERON:0010317!6.74e-07!560;UBERON:0002532!6.74e-07!560;UBERON:0002050!8.98e-07!564
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}}
}}

Revision as of 15:39, 26 November 2012


Full id: C2685_occipital_medial_parietal_hippocampus_amygdala_caudate_temporal



Phase1 CAGE Peaks

Hg19::chr2:210489781..210489790,+p57@MAP2
Hg19::chr3:35786039..35786054,+p1@MIR128-2
Hg19::chr5:175308859..175308869,+p39@CPLX2
Hg19::chrX:18622158..18622169,+p3@CDKL5


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:0043303mast cell degranulation0.016686285279565
GO:0002448mast cell mediated immunity0.016686285279565
GO:0045576mast cell activation0.016686285279565
GO:0043299leukocyte degranulation0.016686285279565
GO:0002444myeloid leukocyte mediated immunity0.016686285279565
GO:0019905syntaxin binding0.01919116716192
GO:0000149SNARE binding0.01919116716192
GO:0007026negative regulation of microtubule depolymerization0.01919116716192
GO:0031114regulation of microtubule depolymerization0.01919116716192
GO:0007019microtubule depolymerization0.01919116716192
GO:0031111negative regulation of microtubule polymerization or depolymerization0.01919116716192
GO:0002274myeloid leukocyte activation0.01919116716192
GO:0031110regulation of microtubule polymerization or depolymerization0.01919116716192
GO:0004693cyclin-dependent protein kinase activity0.01919116716192
GO:0031109microtubule polymerization or depolymerization0.0195536312730498
GO:0006904vesicle docking during exocytosis0.0195536312730498
GO:0048278vesicle docking0.0195536312730498
GO:0022406membrane docking0.0195536312730498
GO:0046777protein amino acid autophosphorylation0.0202839508929141
GO:0051261protein depolymerization0.0202839508929141
GO:0016540protein autoprocessing0.0202839508929141
GO:0051129negative regulation of cellular component organization and biogenesis0.0213340109531962
GO:0045055regulated secretory pathway0.0213340109531962
GO:0006836neurotransmitter transport0.0288641825117031
GO:0002443leukocyte mediated immunity0.0288641825117031
GO:0016485protein processing0.0330935746589501
GO:0051128regulation of cellular component organization and biogenesis0.0330935746589501
GO:0000226microtubule cytoskeleton organization and biogenesis0.0330935746589501
GO:0051248negative regulation of protein metabolic process0.0330935746589501
GO:0002252immune effector process0.0330935746589501
GO:0006887exocytosis0.0330935746589501
GO:0005516calmodulin binding0.0406881110191871
GO:0045321leukocyte activation0.0488306617395578
GO:0005875microtubule associated complex0.0488306617395578



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
telencephalon4.68e-7734
brain grey matter7.62e-7734
gray matter7.62e-7734
cerebral hemisphere2.86e-7632
regional part of telencephalon6.22e-7632
regional part of forebrain4.71e-7341
forebrain4.71e-7341
anterior neural tube4.71e-7341
future forebrain4.71e-7341
regional part of cerebral cortex3.03e-7222
neural tube5.03e-7256
neural rod5.03e-7256
future spinal cord5.03e-7256
neural keel5.03e-7256
regional part of nervous system7.30e-7253
regional part of brain7.30e-7253
neocortex1.33e-6420
central nervous system2.55e-6381
cerebral cortex2.85e-6325
pallium2.85e-6325
nervous system2.68e-5989
brain3.75e-5768
future brain3.75e-5768
pre-chordal neural plate4.34e-4761
neural plate7.66e-4782
presumptive neural plate7.66e-4782
neurectoderm2.64e-4486
ecto-epithelium1.16e-37104
adult organism1.45e-33114
structure with developmental contribution from neural crest7.78e-32132
ectoderm-derived structure2.31e-30171
ectoderm2.31e-30171
presumptive ectoderm2.31e-30171
organ system subdivision4.62e-28223
gyrus1.12e-236
basal ganglion9.32e-219
nuclear complex of neuraxis9.32e-219
aggregate regional part of brain9.32e-219
collection of basal ganglia9.32e-219
cerebral subcortex9.32e-219
occipital lobe2.02e-205
tube2.34e-20192
temporal lobe2.65e-206
limbic system5.20e-205
corpus striatum1.63e-164
striatum1.63e-164
ventral part of telencephalon1.63e-164
future corpus striatum1.63e-164
anatomical conduit1.34e-15240
neural nucleus3.71e-159
nucleus of brain3.71e-159
organ part1.24e-14218
telencephalic nucleus5.39e-147
anatomical cluster9.78e-14373
caudate-putamen4.56e-133
dorsal striatum4.56e-133
parietal lobe5.22e-135
frontal cortex7.07e-133
epithelium3.89e-11306
cell layer6.10e-11309
multi-tissue structure1.49e-10342
Ammon's horn2.81e-092
lobe parts of cerebral cortex2.81e-092
hippocampal formation2.81e-092
limbic lobe2.81e-092
caudate nucleus2.92e-092
future caudate nucleus2.92e-092
middle frontal gyrus3.57e-092
middle temporal gyrus3.87e-092
amygdala5.31e-092
germ layer6.74e-07560
germ layer / neural crest6.74e-07560
embryonic tissue6.74e-07560
presumptive structure6.74e-07560
germ layer / neural crest derived structure6.74e-07560
epiblast (generic)6.74e-07560
embryonic structure8.98e-07564


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)

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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.