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Coexpression cluster:C1112: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.74e-118!56;UBERON:0005068!2.74e-118!56;UBERON:0006241!2.74e-118!56;UBERON:0007135!2.74e-118!56;UBERON:0000073!1.08e-109!53;UBERON:0002616!1.08e-109!53;UBERON:0001017!8.36e-103!81;UBERON:0001016!2.28e-98!89;UBERON:0002780!1.50e-96!41;UBERON:0001890!1.50e-96!41;UBERON:0003080!1.50e-96!41;UBERON:0006240!1.50e-96!41;UBERON:0001893!5.33e-88!34;UBERON:0003528!7.07e-88!34;UBERON:0002020!7.07e-88!34;UBERON:0000955!1.28e-85!68;UBERON:0006238!1.28e-85!68;UBERON:0003075!7.56e-84!82;UBERON:0007284!7.56e-84!82;UBERON:0002791!4.09e-82!32;UBERON:0001869!6.97e-82!32;UBERON:0002346!2.21e-79!86;UBERON:0003056!9.30e-69!61;UBERON:0010371!1.71e-63!104;UBERON:0000956!1.65e-62!25;UBERON:0000203!1.65e-62!25;UBERON:0002619!1.64e-55!22;UBERON:0007023!8.73e-55!114;UBERON:0010314!1.29e-51!132;UBERON:0001950!5.85e-50!20;UBERON:0004121!3.93e-47!171;UBERON:0000924!3.93e-47!171;UBERON:0006601!3.93e-47!171;UBERON:0011216!2.58e-34!223;UBERON:0000025!3.66e-27!192;UBERON:0000125!3.49e-26!9;UBERON:0002308!3.49e-26!9;UBERON:0002420!7.67e-26!9;UBERON:0007245!7.67e-26!9;UBERON:0010009!7.67e-26!9;UBERON:0010011!7.67e-26!9;UBERON:0000454!7.67e-26!9;UBERON:0003076!3.05e-22!15;UBERON:0003057!3.05e-22!15;UBERON:0009663!1.15e-20!7;UBERON:0004111!3.38e-19!240;UBERON:0002298!1.64e-18!6;UBERON:0000064!2.84e-17!218;UBERON:0000200!3.11e-17!6;UBERON:0004732!3.62e-17!13;UBERON:0000477!1.51e-16!373;UBERON:0000349!4.43e-15!5;UBERON:0004733!5.84e-15!12;UBERON:0002028!5.84e-15!12;UBERON:0007277!5.84e-15!12;UBERON:0000483!9.28e-15!306;UBERON:0001872!9.96e-15!5;UBERON:0000119!1.73e-14!309;UBERON:0001871!4.30e-14!6;UBERON:0002021!5.15e-14!5;UBERON:0000369!3.80e-12!4;UBERON:0002435!3.80e-12!4;UBERON:0000204!3.80e-12!4;UBERON:0010082!3.80e-12!4;UBERON:0002784!4.27e-12!4;UBERON:0001894!1.59e-10!7;UBERON:0006222!1.59e-10!7;UBERON:0000481!2.97e-10!342;UBERON:0000988!3.80e-10!3;UBERON:0001896!4.41e-10!3;UBERON:0005290!4.41e-10!3;UBERON:0010096!4.41e-10!3;UBERON:0001870!7.53e-10!3;UBERON:0002240!8.73e-10!3;UBERON:0005174!8.73e-10!3;UBERON:0001137!8.73e-10!3;UBERON:0005383!2.03e-09!3;UBERON:0005382!2.03e-09!3;UBERON:0000062!2.11e-08!503;UBERON:0002680!4.49e-08!9;UBERON:0001895!4.49e-08!9;UBERON:0010092!4.49e-08!9;UBERON:0000923!8.81e-08!560;UBERON:0010316!8.81e-08!560;UBERON:0005291!8.81e-08!560;UBERON:0006598!8.81e-08!560;UBERON:0010317!8.81e-08!560;UBERON:0002532!8.81e-08!560;UBERON:0000922!1.23e-07!592;UBERON:0002050!1.27e-07!564;UBERON:0001897!1.49e-07!2;UBERON:0010225!1.49e-07!2;UBERON:0005423!1.69e-07!581;UBERON:0001875!2.66e-07!2;UBERON:0006514!2.66e-07!2;UBERON:0002148!3.29e-07!2;UBERON:0006331!3.29e-07!2;UBERON:0009662!3.29e-07!2;UBERON:0001954!3.71e-07!2;UBERON:0003022!3.71e-07!2;UBERON:0002421!3.71e-07!2;UBERON:0002600!3.71e-07!2;UBERON:0000467!4.31e-07!624;UBERON:0005162!4.43e-07!2;UBERON:0000122!4.43e-07!2;UBERON:0000480!4.69e-07!625;UBERON:0002702!5.62e-07!2;UBERON:0001876!7.31e-07!2;UBERON:0001873!8.22e-07!2;UBERON:0010122!8.22e-07!2
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}}
}}

Revision as of 14:41, 26 November 2012


Full id: C1112_extraskeletal_corpus_Neural_thalamus_substantia_pons_medulla



Phase1 CAGE Peaks

Hg19::chr10:25304967..25304988,-p2@ENKUR
Hg19::chr16:19612967..19612983,+p7@C16orf62
Hg19::chr16:19896782..19896816,-p4@GPRC5B
Hg19::chr1:66458111..66458123,+p17@PDE4B
Hg19::chr1:66458291..66458304,+p9@PDE4B
Hg19::chr1:66458305..66458316,+p13@PDE4B
Hg19::chrX:43832628..43832644,-p1@NDP


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:0007601visual perception0.00871228837189771
GO:0050953sensory perception of light stimulus0.00871228837189771
GO:0005118sevenless binding0.00871228837189771
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0152438119264595
GO:0001890placenta development0.0261230189931719
GO:0005626insoluble fraction0.0273585139144967
GO:0007033vacuole organization and biogenesis0.0273585139144967
GO:0007600sensory perception0.0371529700088947
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0371529700088947
GO:0005102receptor binding0.0371529700088947
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0371529700088947
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0412847974420979
GO:0050877neurological system process0.0452851199130761



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
astrocyte of the cerebral cortex1.74e-083
Uber Anatomy
Ontology termp-valuen
neural tube2.74e-11856
neural rod2.74e-11856
future spinal cord2.74e-11856
neural keel2.74e-11856
regional part of nervous system1.08e-10953
regional part of brain1.08e-10953
central nervous system8.36e-10381
nervous system2.28e-9889
regional part of forebrain1.50e-9641
forebrain1.50e-9641
anterior neural tube1.50e-9641
future forebrain1.50e-9641
telencephalon5.33e-8834
brain grey matter7.07e-8834
gray matter7.07e-8834
brain1.28e-8568
future brain1.28e-8568
neural plate7.56e-8482
presumptive neural plate7.56e-8482
regional part of telencephalon4.09e-8232
cerebral hemisphere6.97e-8232
neurectoderm2.21e-7986
pre-chordal neural plate9.30e-6961
ecto-epithelium1.71e-63104
cerebral cortex1.65e-6225
pallium1.65e-6225
regional part of cerebral cortex1.64e-5522
adult organism8.73e-55114
structure with developmental contribution from neural crest1.29e-51132
neocortex5.85e-5020
ectoderm-derived structure3.93e-47171
ectoderm3.93e-47171
presumptive ectoderm3.93e-47171
organ system subdivision2.58e-34223
tube3.66e-27192
neural nucleus3.49e-269
nucleus of brain3.49e-269
basal ganglion7.67e-269
nuclear complex of neuraxis7.67e-269
aggregate regional part of brain7.67e-269
collection of basal ganglia7.67e-269
cerebral subcortex7.67e-269
posterior neural tube3.05e-2215
chordal neural plate3.05e-2215
telencephalic nucleus1.15e-207
anatomical conduit3.38e-19240
brainstem1.64e-186
organ part2.84e-17218
gyrus3.11e-176
segmental subdivision of nervous system3.62e-1713
anatomical cluster1.51e-16373
limbic system4.43e-155
segmental subdivision of hindbrain5.84e-1512
hindbrain5.84e-1512
presumptive hindbrain5.84e-1512
epithelium9.28e-15306
parietal lobe9.96e-155
cell layer1.73e-14309
temporal lobe4.30e-146
occipital lobe5.15e-145
corpus striatum3.80e-124
striatum3.80e-124
ventral part of telencephalon3.80e-124
future corpus striatum3.80e-124
regional part of diencephalon4.27e-124
diencephalon1.59e-107
future diencephalon1.59e-107
multi-tissue structure2.97e-10342
pons3.80e-103
medulla oblongata4.41e-103
myelencephalon4.41e-103
future myelencephalon4.41e-103
frontal cortex7.53e-103
spinal cord8.73e-103
dorsal region element8.73e-103
dorsum8.73e-103
caudate-putamen2.03e-093
dorsal striatum2.03e-093
organ2.11e-08503
regional part of metencephalon4.49e-089
metencephalon4.49e-089
future metencephalon4.49e-089
germ layer8.81e-08560
germ layer / neural crest8.81e-08560
embryonic tissue8.81e-08560
presumptive structure8.81e-08560
germ layer / neural crest derived structure8.81e-08560
epiblast (generic)8.81e-08560
embryo1.23e-07592
embryonic structure1.27e-07564
dorsal plus ventral thalamus1.49e-072
thalamic complex1.49e-072
developing anatomical structure1.69e-07581
globus pallidus2.66e-072
pallidum2.66e-072
locus ceruleus3.29e-072
brainstem nucleus3.29e-072
hindbrain nucleus3.29e-072
Ammon's horn3.71e-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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