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|gostat_on_coexpression_clusters=GO:0007601!visual perception!0.00871228837189771!51704;4693$GO:0050953!sensory perception of light stimulus!0.00871228837189771!51704;4693$GO:0005118!sevenless binding!0.00871228837189771!51704$GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.0152438119264595!5142$GO:0001890!placenta development!0.0261230189931719!4693$GO:0005626!insoluble fraction!0.0273585139144967!5142$GO:0007033!vacuole organization and biogenesis!0.0273585139144967!4693$GO:0007600!sensory perception!0.0371529700088947!51704;4693$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0371529700088947!5142$GO:0005102!receptor binding!0.0371529700088947!51704;4693$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0371529700088947!5142$GO:0008067!metabotropic glutamate, GABA-B-like receptor activity!0.0412847974420979!51704$GO:0050877!neurological system process!0.0452851199130761!51704;4693
 
|gostat_on_coexpression_clusters=GO:0007601!visual perception!0.00871228837189771!51704;4693$GO:0050953!sensory perception of light stimulus!0.00871228837189771!51704;4693$GO:0005118!sevenless binding!0.00871228837189771!51704$GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.0152438119264595!5142$GO:0001890!placenta development!0.0261230189931719!4693$GO:0005626!insoluble fraction!0.0273585139144967!5142$GO:0007033!vacuole organization and biogenesis!0.0273585139144967!4693$GO:0007600!sensory perception!0.0371529700088947!51704;4693$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0371529700088947!5142$GO:0005102!receptor binding!0.0371529700088947!51704;4693$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0371529700088947!5142$GO:0008067!metabotropic glutamate, GABA-B-like receptor activity!0.0412847974420979!51704$GO:0050877!neurological system process!0.0452851199130761!51704;4693
 
|id=C1112
 
|id=C1112
 +
|ontology_enrichment_celltype=
 +
|ontology_enrichment_disease=
 +
|ontology_enrichment_uberon=UBERON:0001049!6.95e-45!57;UBERON:0005068!6.95e-45!57;UBERON:0006241!6.95e-45!57;UBERON:0007135!6.95e-45!57;UBERON:0005743!2.53e-41!86;UBERON:0001017!4.74e-41!82;UBERON:0000073!6.72e-40!94;UBERON:0001016!6.72e-40!94;UBERON:0002616!1.02e-37!59;UBERON:0007023!7.11e-37!115;UBERON:0000955!7.74e-36!69;UBERON:0006238!7.74e-36!69;UBERON:0002780!8.00e-35!41;UBERON:0001890!8.00e-35!41;UBERON:0006240!8.00e-35!41;UBERON:0003075!1.03e-33!86;UBERON:0007284!1.03e-33!86;UBERON:0003080!1.67e-33!42;UBERON:0002346!5.24e-33!90;UBERON:0001893!1.06e-29!34;UBERON:0002020!1.20e-29!34;UBERON:0003528!1.20e-29!34;UBERON:0002791!8.38e-29!33;UBERON:0001869!8.28e-28!32;UBERON:0004121!1.57e-25!169;UBERON:0000924!1.76e-25!173;UBERON:0006601!1.76e-25!173;UBERON:0003056!2.76e-24!61;UBERON:0000153!7.54e-23!129;UBERON:0007811!7.54e-23!129;UBERON:0000033!2.45e-22!123;UBERON:0000956!8.18e-22!25;UBERON:0000203!8.18e-22!25;UBERON:0002619!1.31e-19!22;UBERON:0001950!6.51e-18!20;UBERON:0000922!2.78e-13!612;UBERON:0002050!6.20e-13!605;UBERON:0005423!6.20e-13!605;UBERON:0000923!1.53e-12!604;UBERON:0005291!1.53e-12!604;UBERON:0006598!1.53e-12!604;UBERON:0002532!1.53e-12!604;UBERON:0003076!3.43e-12!15;UBERON:0003057!3.43e-12!15;UBERON:0000025!8.48e-12!194;UBERON:0000467!1.08e-11!625;UBERON:0000480!1.47e-11!626;UBERON:0000468!1.46e-10!659;UBERON:0004732!1.78e-10!13;UBERON:0000062!2.01e-10!511;UBERON:0004111!2.80e-10!241;UBERON:0000483!4.74e-10!309;UBERON:0004733!9.61e-10!12;UBERON:0002028!9.61e-10!12;UBERON:0007277!9.61e-10!12;UBERON:0000119!1.32e-09!312;UBERON:0002308!3.05e-09!9;UBERON:0000125!3.05e-09!9;UBERON:0002420!4.05e-09!9;UBERON:0007245!4.05e-09!9;UBERON:0010009!4.05e-09!9;UBERON:0010011!4.05e-09!9;UBERON:0000454!4.05e-09!9;UBERON:0000475!4.79e-09!365;UBERON:0000477!1.20e-08!286;UBERON:0000064!1.18e-07!219;UBERON:0001871!1.54e-07!7;UBERON:0009663!1.66e-07!7;UBERON:0002680!3.40e-07!9;UBERON:0001895!3.40e-07!9;UBERON:0010092!3.40e-07!9
 
}}
 
}}

Revision as of 05:07, 21 May 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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube6.95e-4557
neural rod6.95e-4557
future spinal cord6.95e-4557
neural keel6.95e-4557
central nervous system4.74e-4182
regional part of nervous system6.72e-4094
nervous system6.72e-4094
regional part of brain1.02e-3759
adult organism7.11e-37115
brain7.74e-3669
future brain7.74e-3669
regional part of forebrain8.00e-3541
forebrain8.00e-3541
future forebrain8.00e-3541
neural plate1.03e-3386
presumptive neural plate1.03e-3386
anterior neural tube1.67e-3342
neurectoderm5.24e-3390
telencephalon1.06e-2934
gray matter1.20e-2934
brain grey matter1.20e-2934
regional part of telencephalon8.38e-2933
cerebral hemisphere8.28e-2832
ectoderm-derived structure1.57e-25169
ectoderm1.76e-25173
presumptive ectoderm1.76e-25173
pre-chordal neural plate2.76e-2461
anterior region of body7.54e-23129
craniocervical region7.54e-23129
head2.45e-22123
cerebral cortex8.18e-2225
pallium8.18e-2225
regional part of cerebral cortex1.31e-1922
neocortex6.51e-1820
embryo2.78e-13612
embryonic structure6.20e-13605
developing anatomical structure6.20e-13605
germ layer1.53e-12604
embryonic tissue1.53e-12604
presumptive structure1.53e-12604
epiblast (generic)1.53e-12604
posterior neural tube3.43e-1215
chordal neural plate3.43e-1215
tube8.48e-12194
anatomical system1.08e-11625
anatomical group1.47e-11626
multi-cellular organism1.46e-10659
segmental subdivision of nervous system1.78e-1013
organ2.01e-10511
anatomical conduit2.80e-10241
epithelium4.74e-10309
segmental subdivision of hindbrain9.61e-1012
hindbrain9.61e-1012
presumptive hindbrain9.61e-1012
cell layer1.32e-09312
nucleus of brain3.05e-099
neural nucleus3.05e-099
basal ganglion4.05e-099
nuclear complex of neuraxis4.05e-099
aggregate regional part of brain4.05e-099
collection of basal ganglia4.05e-099
cerebral subcortex4.05e-099
organism subdivision4.79e-09365
anatomical cluster1.20e-08286
organ part1.18e-07219
temporal lobe1.54e-077
telencephalic nucleus1.66e-077
regional part of metencephalon3.40e-079
metencephalon3.40e-079
future metencephalon3.40e-079


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.