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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.77e-46!82;UBERON:0005743!1.56e-45!86;UBERON:0001049!2.89e-43!57;UBERON:0005068!2.89e-43!57;UBERON:0006241!2.89e-43!57;UBERON:0007135!2.89e-43!57;UBERON:0000073!8.96e-41!94;UBERON:0001016!8.96e-41!94;UBERON:0002616!1.59e-39!59;UBERON:0003075!2.85e-39!86;UBERON:0007284!2.85e-39!86;UBERON:0002346!1.25e-38!90;UBERON:0000955!7.06e-37!69;UBERON:0006238!7.06e-37!69;UBERON:0002780!5.78e-35!41;UBERON:0001890!5.78e-35!41;UBERON:0006240!5.78e-35!41;UBERON:0003080!1.12e-33!42;UBERON:0003056!9.70e-33!61;UBERON:0007023!6.00e-31!115;UBERON:0000033!2.31e-30!123;UBERON:0000153!3.71e-30!129;UBERON:0007811!3.71e-30!129;UBERON:0002020!9.78e-30!34;UBERON:0003528!9.78e-30!34;UBERON:0001893!2.72e-29!34;UBERON:0001869!1.36e-28!32;UBERON:0002791!2.15e-28!33;UBERON:0000924!3.15e-28!173;UBERON:0006601!3.15e-28!173;UBERON:0004121!3.75e-28!169;UBERON:0000956!3.89e-23!25;UBERON:0000203!3.89e-23!25;UBERON:0002619!1.80e-21!22;UBERON:0001950!1.23e-19!20;UBERON:0000064!4.36e-13!219;UBERON:0003076!1.55e-10!15;UBERON:0003057!1.55e-10!15;UBERON:0000025!5.82e-09!194;UBERON:0000062!6.32e-09!511;UBERON:0000475!7.87e-09!365;UBERON:0004733!1.30e-08!12;UBERON:0002028!1.30e-08!12;UBERON:0007277!1.30e-08!12;UBERON:0001871!1.55e-08!7;UBERON:0000922!3.06e-08!612;UBERON:0002308!5.03e-08!9;UBERON:0000125!5.03e-08!9;UBERON:0002420!5.21e-08!9;UBERON:0007245!5.21e-08!9;UBERON:0010009!5.21e-08!9;UBERON:0010011!5.21e-08!9;UBERON:0000454!5.21e-08!9;UBERON:0000477!7.49e-08!286;UBERON:0000468!1.07e-07!659;UBERON:0004732!1.22e-07!13;UBERON:0000481!1.43e-07!347;UBERON:0000119!2.25e-07!312;UBERON:0004111!2.81e-07!241;UBERON:0001894!5.06e-07!7;UBERON:0006222!5.06e-07!7;UBERON:0000483!9.56e-07!309
|ontology_enrichment_uberon=UBERON:0001017!2.77e-46!82;UBERON:0005743!1.56e-45!86;UBERON:0001049!2.89e-43!57;UBERON:0005068!2.89e-43!57;UBERON:0006241!2.89e-43!57;UBERON:0007135!2.89e-43!57;UBERON:0000073!8.96e-41!94;UBERON:0001016!8.96e-41!94;UBERON:0002616!1.59e-39!59;UBERON:0003075!2.85e-39!86;UBERON:0007284!2.85e-39!86;UBERON:0002346!1.25e-38!90;UBERON:0000955!7.06e-37!69;UBERON:0006238!7.06e-37!69;UBERON:0002780!5.78e-35!41;UBERON:0001890!5.78e-35!41;UBERON:0006240!5.78e-35!41;UBERON:0003080!1.12e-33!42;UBERON:0003056!9.70e-33!61;UBERON:0007023!6.00e-31!115;UBERON:0000033!2.31e-30!123;UBERON:0000153!3.71e-30!129;UBERON:0007811!3.71e-30!129;UBERON:0002020!9.78e-30!34;UBERON:0003528!9.78e-30!34;UBERON:0001893!2.72e-29!34;UBERON:0001869!1.36e-28!32;UBERON:0002791!2.15e-28!33;UBERON:0000924!3.15e-28!173;UBERON:0006601!3.15e-28!173;UBERON:0004121!3.75e-28!169;UBERON:0000956!3.89e-23!25;UBERON:0000203!3.89e-23!25;UBERON:0002619!1.80e-21!22;UBERON:0001950!1.23e-19!20;UBERON:0000064!4.36e-13!219;UBERON:0003076!1.55e-10!15;UBERON:0003057!1.55e-10!15;UBERON:0000025!5.82e-09!194;UBERON:0000062!6.32e-09!511;UBERON:0000475!7.87e-09!365;UBERON:0004733!1.30e-08!12;UBERON:0002028!1.30e-08!12;UBERON:0007277!1.30e-08!12;UBERON:0001871!1.55e-08!7;UBERON:0000922!3.06e-08!612;UBERON:0002308!5.03e-08!9;UBERON:0000125!5.03e-08!9;UBERON:0002420!5.21e-08!9;UBERON:0007245!5.21e-08!9;UBERON:0010009!5.21e-08!9;UBERON:0010011!5.21e-08!9;UBERON:0000454!5.21e-08!9;UBERON:0000477!7.49e-08!286;UBERON:0000468!1.07e-07!659;UBERON:0004732!1.22e-07!13;UBERON:0000481!1.43e-07!347;UBERON:0000119!2.25e-07!312;UBERON:0004111!2.81e-07!241;UBERON:0001894!5.06e-07!7;UBERON:0006222!5.06e-07!7;UBERON:0000483!9.56e-07!309
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}}
}}

Revision as of 12:02, 5 September 2012


Full id: C899_pituitary_cerebellum_occipital_parietal_testicular_brain_temporal



Phase1 CAGE Peaks

Hg19::chr13:26042960..26043015,+p2@ATP8A2
Hg19::chr14:74185796..74185825,-p1@AK308604
Hg19::chr16:2136434..2136445,+p@chr16:2136434..2136445
+
Hg19::chr16:87369953..87369959,-p@chr16:87369953..87369959
-
Hg19::chr2:203735519..203735539,-p8@ICA1L
Hg19::chr2:203735586..203735600,-p14@ICA1L
Hg19::chr9:14662234..14662273,-p@chr9:14662234..14662273
-
Hg19::chr9:74061853..74061893,-p7@TRPM3
Hg19::chr9:74061895..74061905,-p14@TRPM3


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:0004012phospholipid-translocating ATPase activity0.0218266084661406
GO:0015247aminophospholipid transporter activity0.0218266084661406
GO:0015914phospholipid transport0.0218266084661406
GO:0015075ion transmembrane transporter activity0.0218266084661406
GO:0005548phospholipid transporter activity0.0218266084661406
GO:0022891substrate-specific transmembrane transporter activity0.0218266084661406
GO:0022857transmembrane transporter activity0.0218266084661406
GO:0022892substrate-specific transporter activity0.0222822945446405
GO:0005319lipid transporter activity0.0413879448357098
GO:0005262calcium channel activity0.0461577732564526
GO:0006869lipid transport0.0468509204505933
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0468509204505933
GO:0006816calcium ion transport0.0488370558464889
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0488370558464889
GO:0008285negative regulation of cell proliferation0.0488370558464889
GO:0006810transport0.0488370558464889
GO:0015674di-, tri-valent inorganic cation transport0.0488370558464889
GO:0051234establishment of localization0.0488370558464889
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0488370558464889
GO:0043492ATPase activity, coupled to movement of substances0.0488370558464889
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0488370558464889
GO:0051179localization0.0488370558464889
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0488370558464889
GO:0015399primary active transmembrane transporter activity0.0488370558464889



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 cell2.24e-078
Uber Anatomy
Ontology termp-valuen
central nervous system2.77e-4682
neural tube2.89e-4357
neural rod2.89e-4357
future spinal cord2.89e-4357
neural keel2.89e-4357
regional part of nervous system8.96e-4194
nervous system8.96e-4194
regional part of brain1.59e-3959
neural plate2.85e-3986
presumptive neural plate2.85e-3986
neurectoderm1.25e-3890
brain7.06e-3769
future brain7.06e-3769
regional part of forebrain5.78e-3541
forebrain5.78e-3541
future forebrain5.78e-3541
anterior neural tube1.12e-3342
pre-chordal neural plate9.70e-3361
adult organism6.00e-31115
head2.31e-30123
anterior region of body3.71e-30129
craniocervical region3.71e-30129
gray matter9.78e-3034
brain grey matter9.78e-3034
telencephalon2.72e-2934
cerebral hemisphere1.36e-2832
regional part of telencephalon2.15e-2833
ectoderm3.15e-28173
presumptive ectoderm3.15e-28173
ectoderm-derived structure3.75e-28169
cerebral cortex3.89e-2325
pallium3.89e-2325
regional part of cerebral cortex1.80e-2122
neocortex1.23e-1920
organ part4.36e-13219
posterior neural tube1.55e-1015
chordal neural plate1.55e-1015
tube5.82e-09194
organ6.32e-09511
organism subdivision7.87e-09365
segmental subdivision of hindbrain1.30e-0812
hindbrain1.30e-0812
presumptive hindbrain1.30e-0812
temporal lobe1.55e-087
embryo3.06e-08612
nucleus of brain5.03e-089
neural nucleus5.03e-089
basal ganglion5.21e-089
nuclear complex of neuraxis5.21e-089
aggregate regional part of brain5.21e-089
collection of basal ganglia5.21e-089
cerebral subcortex5.21e-089
anatomical cluster7.49e-08286
multi-cellular organism1.07e-07659
segmental subdivision of nervous system1.22e-0713
multi-tissue structure1.43e-07347
cell layer2.25e-07312
anatomical conduit2.81e-07241
diencephalon5.06e-077
future diencephalon5.06e-077
epithelium9.56e-07309


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
RAD21#588544.602237286869480.007351242900196250.0303965657317917



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.