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Coexpression cluster:C1620: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!5.13e-57!56;UBERON:0005068!5.13e-57!56;UBERON:0006241!5.13e-57!56;UBERON:0007135!5.13e-57!56;UBERON:0000073!8.78e-52!53;UBERON:0002616!8.78e-52!53;UBERON:0001017!2.02e-45!81;UBERON:0003075!5.07e-43!82;UBERON:0007284!5.07e-43!82;UBERON:0001016!1.07e-42!89;UBERON:0003528!2.03e-41!34;UBERON:0002020!2.03e-41!34;UBERON:0001893!3.81e-41!34;UBERON:0002780!8.11e-41!41;UBERON:0001890!8.11e-41!41;UBERON:0003080!8.11e-41!41;UBERON:0006240!8.11e-41!41;UBERON:0000955!1.06e-40!68;UBERON:0006238!1.06e-40!68;UBERON:0002346!2.83e-40!86;UBERON:0002791!4.20e-38!32;UBERON:0001869!9.31e-38!32;UBERON:0010371!7.22e-35!104;UBERON:0003056!1.13e-30!61;UBERON:0010314!6.81e-30!132;UBERON:0000956!3.16e-27!25;UBERON:0000203!3.16e-27!25;UBERON:0002619!6.63e-26!22;UBERON:0007023!1.03e-23!114;UBERON:0001950!8.99e-23!20;UBERON:0004121!1.09e-22!171;UBERON:0000924!1.09e-22!171;UBERON:0006601!1.09e-22!171;UBERON:0000025!1.82e-20!192;UBERON:0003076!9.34e-17!15;UBERON:0003057!9.34e-17!15;UBERON:0004111!2.71e-16!240;UBERON:0002420!5.15e-16!9;UBERON:0007245!5.15e-16!9;UBERON:0010009!5.15e-16!9;UBERON:0010011!5.15e-16!9;UBERON:0000454!5.15e-16!9;UBERON:0000483!5.32e-16!306;UBERON:0000125!6.03e-16!9;UBERON:0002308!6.03e-16!9;UBERON:0000119!1.23e-15!309;UBERON:0011216!4.93e-14!223;UBERON:0009663!1.22e-12!7;UBERON:0000477!1.57e-12!373;UBERON:0002298!7.37e-12!6;UBERON:0004733!7.81e-12!12;UBERON:0002028!7.81e-12!12;UBERON:0007277!7.81e-12!12;UBERON:0000200!3.75e-11!6;UBERON:0000064!5.58e-11!218;UBERON:0004732!9.53e-11!13;UBERON:0000349!1.35e-09!5;UBERON:0001871!1.59e-09!6;UBERON:0002050!1.01e-07!564;UBERON:0000481!1.02e-07!342;UBERON:0000369!1.20e-07!4;UBERON:0002435!1.20e-07!4;UBERON:0000204!1.20e-07!4;UBERON:0010082!1.20e-07!4;UBERON:0000923!1.65e-07!560;UBERON:0010316!1.65e-07!560;UBERON:0005291!1.65e-07!560;UBERON:0006598!1.65e-07!560;UBERON:0010317!1.65e-07!560;UBERON:0002532!1.65e-07!560;UBERON:0002680!3.10e-07!9;UBERON:0001895!3.10e-07!9;UBERON:0010092!3.10e-07!9;UBERON:0002240!5.83e-07!3;UBERON:0005174!5.83e-07!3;UBERON:0001137!5.83e-07!3;UBERON:0001896!7.58e-07!3;UBERON:0005290!7.58e-07!3;UBERON:0010096!7.58e-07!3;UBERON:0005423!8.82e-07!581;UBERON:0002021!9.16e-07!5;UBERON:0000468!9.52e-07!656
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1620_spinal_occipital_optic_diencephalon_substantia_brain_corpus



Phase1 CAGE Peaks

Hg19::chr11:125366047..125366076,-p5@FEZ1
Hg19::chr11:125366089..125366207,-p1@FEZ1
Hg19::chr17:40126302..40126313,+p6@BC148241
Hg19::chr17:42984454..42984463,-p37@GFAP
Hg19::chr4:83551834..83551855,-p@chr4:83551834..83551855
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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:0043015gamma-tubulin binding0.0207887046966037
GO:0044430cytoskeletal part0.0207887046966037
GO:0005856cytoskeleton0.0322259237004165
GO:0007411axon guidance0.0322259237004165
GO:0015631tubulin binding0.0322259237004165
GO:0005200structural constituent of cytoskeleton0.0322259237004165
GO:0007409axonogenesis0.0322259237004165
GO:0048667neuron morphogenesis during differentiation0.0322259237004165
GO:0048812neurite morphogenesis0.0322259237004165
GO:0043232intracellular non-membrane-bound organelle0.0322259237004165
GO:0043228non-membrane-bound organelle0.0322259237004165
GO:0000904cellular morphogenesis during differentiation0.0322259237004165
GO:0005813centrosome0.0322259237004165
GO:0031175neurite development0.0322259237004165
GO:0005815microtubule organizing center0.0322259237004165
GO:0048666neuron development0.0322259237004165
GO:0032990cell part morphogenesis0.0323941803318015
GO:0048858cell projection morphogenesis0.0323941803318015
GO:0030030cell projection organization and biogenesis0.0323941803318015
GO:0030182neuron differentiation0.0323941803318015
GO:0016477cell migration0.0323941803318015
GO:0045111intermediate filament cytoskeleton0.0323941803318015
GO:0005882intermediate filament0.0323941803318015
GO:0048699generation of neurons0.0323941803318015
GO:0044446intracellular organelle part0.0323941803318015
GO:0044422organelle part0.0323941803318015
GO:0022008neurogenesis0.0324376738613004
GO:0051674localization of cell0.0440692668892321
GO:0006928cell motility0.0440692668892321



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 tube5.13e-5756
neural rod5.13e-5756
future spinal cord5.13e-5756
neural keel5.13e-5756
regional part of nervous system8.78e-5253
regional part of brain8.78e-5253
central nervous system2.02e-4581
neural plate5.07e-4382
presumptive neural plate5.07e-4382
nervous system1.07e-4289
brain grey matter2.03e-4134
gray matter2.03e-4134
telencephalon3.81e-4134
regional part of forebrain8.11e-4141
forebrain8.11e-4141
anterior neural tube8.11e-4141
future forebrain8.11e-4141
brain1.06e-4068
future brain1.06e-4068
neurectoderm2.83e-4086
regional part of telencephalon4.20e-3832
cerebral hemisphere9.31e-3832
ecto-epithelium7.22e-35104
pre-chordal neural plate1.13e-3061
structure with developmental contribution from neural crest6.81e-30132
cerebral cortex3.16e-2725
pallium3.16e-2725
regional part of cerebral cortex6.63e-2622
adult organism1.03e-23114
neocortex8.99e-2320
ectoderm-derived structure1.09e-22171
ectoderm1.09e-22171
presumptive ectoderm1.09e-22171
tube1.82e-20192
posterior neural tube9.34e-1715
chordal neural plate9.34e-1715
anatomical conduit2.71e-16240
basal ganglion5.15e-169
nuclear complex of neuraxis5.15e-169
aggregate regional part of brain5.15e-169
collection of basal ganglia5.15e-169
cerebral subcortex5.15e-169
epithelium5.32e-16306
neural nucleus6.03e-169
nucleus of brain6.03e-169
cell layer1.23e-15309
organ system subdivision4.93e-14223
telencephalic nucleus1.22e-127
anatomical cluster1.57e-12373
brainstem7.37e-126
segmental subdivision of hindbrain7.81e-1212
hindbrain7.81e-1212
presumptive hindbrain7.81e-1212
gyrus3.75e-116
organ part5.58e-11218
segmental subdivision of nervous system9.53e-1113
limbic system1.35e-095
temporal lobe1.59e-096
embryonic structure1.01e-07564
multi-tissue structure1.02e-07342
corpus striatum1.20e-074
striatum1.20e-074
ventral part of telencephalon1.20e-074
future corpus striatum1.20e-074
germ layer1.65e-07560
germ layer / neural crest1.65e-07560
embryonic tissue1.65e-07560
presumptive structure1.65e-07560
germ layer / neural crest derived structure1.65e-07560
epiblast (generic)1.65e-07560
regional part of metencephalon3.10e-079
metencephalon3.10e-079
future metencephalon3.10e-079
spinal cord5.83e-073
dorsal region element5.83e-073
dorsum5.83e-073
medulla oblongata7.58e-073
myelencephalon7.58e-073
future myelencephalon7.58e-073
developing anatomical structure8.82e-07581
occipital lobe9.16e-075
multi-cellular organism9.52e-07656


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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