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Coexpression cluster:C1643: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.88e-52!115;UBERON:0001049!1.25e-31!57;UBERON:0005068!1.25e-31!57;UBERON:0006241!1.25e-31!57;UBERON:0007135!1.25e-31!57;UBERON:0002616!8.00e-30!59;UBERON:0001017!3.57e-29!82;UBERON:0000073!9.70e-29!94;UBERON:0001016!9.70e-29!94;UBERON:0005743!4.19e-28!86;UBERON:0002346!4.23e-27!90;UBERON:0000955!7.79e-27!69;UBERON:0006238!7.79e-27!69;UBERON:0003075!1.64e-26!86;UBERON:0007284!1.64e-26!86;UBERON:0003080!1.40e-24!42;UBERON:0002780!4.19e-24!41;UBERON:0001890!4.19e-24!41;UBERON:0006240!4.19e-24!41;UBERON:0000924!2.12e-22!173;UBERON:0006601!2.12e-22!173;UBERON:0004121!1.13e-21!169;UBERON:0000477!2.29e-20!286;UBERON:0002020!3.40e-20!34;UBERON:0003528!3.40e-20!34;UBERON:0000153!4.16e-20!129;UBERON:0007811!4.16e-20!129;UBERON:0001893!4.22e-20!34;UBERON:0000033!5.28e-20!123;UBERON:0002791!1.41e-19!33;UBERON:0004111!7.37e-19!241;UBERON:0003056!8.09e-19!61;UBERON:0001869!8.72e-19!32;UBERON:0000119!2.19e-17!312;UBERON:0000483!4.67e-17!309;UBERON:0000481!2.77e-16!347;UBERON:0000025!3.44e-16!194;UBERON:0000475!8.67e-15!365;UBERON:0000956!1.09e-14!25;UBERON:0000203!1.09e-14!25;UBERON:0002619!4.31e-14!22;UBERON:0001950!7.09e-13!20;UBERON:0000468!2.23e-12!659;UBERON:0002050!1.22e-11!605;UBERON:0005423!1.22e-11!605;UBERON:0000923!2.47e-11!604;UBERON:0005291!2.47e-11!604;UBERON:0006598!2.47e-11!604;UBERON:0002532!2.47e-11!604;UBERON:0000922!3.43e-11!612;UBERON:0000467!1.58e-10!625;UBERON:0000480!2.63e-10!626;UBERON:0000064!2.58e-09!219;UBERON:0003076!3.55e-08!15;UBERON:0003057!3.55e-08!15;UBERON:0000062!2.04e-07!511;UBERON:0002308!5.36e-07!9;UBERON:0000125!5.36e-07!9;UBERON:0004732!5.86e-07!13;UBERON:0002420!7.74e-07!9;UBERON:0007245!7.74e-07!9;UBERON:0010009!7.74e-07!9;UBERON:0010011!7.74e-07!9;UBERON:0000454!7.74e-07!9
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}}
}}

Revision as of 17:30, 8 August 2012


Full id: C1643_cerebellum_breast_pineal_spinal_acute_hippocampus_medulla



Phase1 CAGE Peaks

Hg19::chr11:71791726..71791756,-p8@NUMA1
Hg19::chr1:150039659..150039684,-p@chr1:150039659..150039684
-
Hg19::chr1:61547894..61547968,+p2@NFIA
Hg19::chr1:61548069..61548102,+p3@NFIA
Hg19::chr1:61548118..61548129,+p9@NFIA


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:0051322anaphase0.0108906810524625
GO:0000090mitotic anaphase0.0108906810524625
GO:0005876spindle microtubule0.0197881225581302
GO:0019079viral genome replication0.0197881225581302
GO:0000922spindle pole0.0197881225581302
GO:0043025cell soma0.0197881225581302
GO:0006997nuclear organization and biogenesis0.0197881225581302
GO:0030425dendrite0.0197881225581302
GO:0016363nuclear matrix0.0197881225581302
GO:0008017microtubule binding0.0197881225581302
GO:0019058viral infectious cycle0.0197881225581302
GO:0022415viral reproductive process0.0206764560402455
GO:0015631tubulin binding0.0220289584636577
GO:0051321meiotic cell cycle0.0220289584636577
GO:0005819spindle0.0220289584636577
GO:0043005neuron projection0.0220289584636577



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
adult organism6.88e-52115
neural tube1.25e-3157
neural rod1.25e-3157
future spinal cord1.25e-3157
neural keel1.25e-3157
regional part of brain8.00e-3059
central nervous system3.57e-2982
regional part of nervous system9.70e-2994
nervous system9.70e-2994
neurectoderm4.23e-2790
brain7.79e-2769
future brain7.79e-2769
neural plate1.64e-2686
presumptive neural plate1.64e-2686
anterior neural tube1.40e-2442
regional part of forebrain4.19e-2441
forebrain4.19e-2441
future forebrain4.19e-2441
ectoderm2.12e-22173
presumptive ectoderm2.12e-22173
ectoderm-derived structure1.13e-21169
anatomical cluster2.29e-20286
gray matter3.40e-2034
brain grey matter3.40e-2034
anterior region of body4.16e-20129
craniocervical region4.16e-20129
telencephalon4.22e-2034
head5.28e-20123
regional part of telencephalon1.41e-1933
anatomical conduit7.37e-19241
pre-chordal neural plate8.09e-1961
cerebral hemisphere8.72e-1932
cell layer2.19e-17312
epithelium4.67e-17309
multi-tissue structure2.77e-16347
tube3.44e-16194
organism subdivision8.67e-15365
cerebral cortex1.09e-1425
pallium1.09e-1425
regional part of cerebral cortex4.31e-1422
neocortex7.09e-1320
multi-cellular organism2.23e-12659
embryonic structure1.22e-11605
developing anatomical structure1.22e-11605
germ layer2.47e-11604
embryonic tissue2.47e-11604
presumptive structure2.47e-11604
epiblast (generic)2.47e-11604
embryo3.43e-11612
anatomical system1.58e-10625
anatomical group2.63e-10626
organ part2.58e-09219
posterior neural tube3.55e-0815
chordal neural plate3.55e-0815
organ2.04e-07511
nucleus of brain5.36e-079
neural nucleus5.36e-079
segmental subdivision of nervous system5.86e-0713
basal ganglion7.74e-079
nuclear complex of neuraxis7.74e-079
aggregate regional part of brain7.74e-079
collection of basal ganglia7.74e-079
cerebral subcortex7.74e-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.

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