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Coexpression cluster:C550: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.22e-46!115;UBERON:0001049!2.23e-35!57;UBERON:0005068!2.23e-35!57;UBERON:0006241!2.23e-35!57;UBERON:0007135!2.23e-35!57;UBERON:0003075!8.09e-32!86;UBERON:0007284!8.09e-32!86;UBERON:0001017!4.07e-31!82;UBERON:0002616!5.72e-31!59;UBERON:0002346!2.18e-30!90;UBERON:0005743!5.22e-30!86;UBERON:0000955!1.23e-27!69;UBERON:0006238!1.23e-27!69;UBERON:0003080!9.61e-27!42;UBERON:0002780!2.58e-26!41;UBERON:0001890!2.58e-26!41;UBERON:0006240!2.58e-26!41;UBERON:0000073!9.02e-26!94;UBERON:0001016!9.02e-26!94;UBERON:0000153!1.96e-25!129;UBERON:0007811!1.96e-25!129;UBERON:0000033!2.98e-25!123;UBERON:0003056!2.02e-23!61;UBERON:0001893!2.68e-22!34;UBERON:0002020!2.74e-22!34;UBERON:0003528!2.74e-22!34;UBERON:0000477!5.22e-22!286;UBERON:0004111!6.99e-22!241;UBERON:0002791!1.06e-21!33;UBERON:0004121!1.65e-21!169;UBERON:0000924!5.23e-21!173;UBERON:0006601!5.23e-21!173;UBERON:0001869!6.12e-21!32;UBERON:0000025!7.20e-17!194;UBERON:0000956!2.12e-16!25;UBERON:0000203!2.12e-16!25;UBERON:0000483!1.60e-15!309;UBERON:0000119!1.80e-15!312;UBERON:0002619!3.81e-15!22;UBERON:0000475!3.88e-15!365;UBERON:0001950!8.67e-14!20;UBERON:0000481!5.50e-13!347;UBERON:0000468!1.51e-12!659;UBERON:0000480!1.46e-11!626;UBERON:0000922!1.64e-11!612;UBERON:0000467!2.06e-11!625;UBERON:0002050!2.78e-10!605;UBERON:0005423!2.78e-10!605;UBERON:0000923!5.12e-10!604;UBERON:0005291!5.12e-10!604;UBERON:0006598!5.12e-10!604;UBERON:0002532!5.12e-10!604;UBERON:0000064!7.40e-10!219;UBERON:0003076!1.21e-09!15;UBERON:0003057!1.21e-09!15;UBERON:0004732!2.14e-08!13;UBERON:0000062!2.30e-08!511;UBERON:0004733!8.43e-08!12;UBERON:0002028!8.43e-08!12;UBERON:0007277!8.43e-08!12;UBERON:0002420!1.65e-07!9;UBERON:0007245!1.65e-07!9;UBERON:0010009!1.65e-07!9;UBERON:0010011!1.65e-07!9;UBERON:0000454!1.65e-07!9;UBERON:0002308!2.35e-07!9;UBERON:0000125!2.35e-07!9
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}}
}}

Revision as of 20:30, 8 August 2012


Full id: C550_hippocampus_amygdala_globus_medial_occipital_thalamus_middle



Phase1 CAGE Peaks

Hg19::chr3:58551312..58551323,-p@chr3:58551312..58551323
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Hg19::chr3:58551381..58551392,-p@chr3:58551381..58551392
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Hg19::chr3:58551652..58551663,-p@chr3:58551652..58551663
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Hg19::chr3:58551759..58551769,-p@chr3:58551759..58551769
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Hg19::chr3:58551789..58551800,-p@chr3:58551789..58551800
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Hg19::chr3:58552053..58552068,-p@chr3:58552053..58552068
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Hg19::chr3:58552082..58552096,-p@chr3:58552082..58552096
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Hg19::chr3:58552139..58552144,-p@chr3:58552139..58552144
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Hg19::chr3:58552163..58552174,-p@chr3:58552163..58552174
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Hg19::chr3:58552313..58552322,-p@chr3:58552313..58552322
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Hg19::chr3:58553081..58553093,-p@chr3:58553081..58553093
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Hg19::chr3:58563295..58563305,-p10@FAM107A
Hg19::chr3:58613256..58613263,-p18@FAM107A
Hg19::chr3:58613294..58613306,-p7@FAM107A
Hg19::chr3:58613323..58613342,-p4@FAM107A
Hg19::chr4:83601902..83601920,-p4@SCD5
Hg19::chr7:139416168..139416220,-p@chr7:139416168..139416220
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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:0004768stearoyl-CoA 9-desaturase activity0.0141286590560376
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.0211904930526434



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 organism1.22e-46115
neural tube2.23e-3557
neural rod2.23e-3557
future spinal cord2.23e-3557
neural keel2.23e-3557
neural plate8.09e-3286
presumptive neural plate8.09e-3286
central nervous system4.07e-3182
regional part of brain5.72e-3159
neurectoderm2.18e-3090
brain1.23e-2769
future brain1.23e-2769
anterior neural tube9.61e-2742
regional part of forebrain2.58e-2641
forebrain2.58e-2641
future forebrain2.58e-2641
regional part of nervous system9.02e-2694
nervous system9.02e-2694
anterior region of body1.96e-25129
craniocervical region1.96e-25129
head2.98e-25123
pre-chordal neural plate2.02e-2361
telencephalon2.68e-2234
gray matter2.74e-2234
brain grey matter2.74e-2234
anatomical cluster5.22e-22286
anatomical conduit6.99e-22241
regional part of telencephalon1.06e-2133
ectoderm-derived structure1.65e-21169
ectoderm5.23e-21173
presumptive ectoderm5.23e-21173
cerebral hemisphere6.12e-2132
tube7.20e-17194
cerebral cortex2.12e-1625
pallium2.12e-1625
epithelium1.60e-15309
cell layer1.80e-15312
regional part of cerebral cortex3.81e-1522
organism subdivision3.88e-15365
neocortex8.67e-1420
multi-tissue structure5.50e-13347
multi-cellular organism1.51e-12659
anatomical group1.46e-11626
embryo1.64e-11612
anatomical system2.06e-11625
embryonic structure2.78e-10605
developing anatomical structure2.78e-10605
germ layer5.12e-10604
embryonic tissue5.12e-10604
presumptive structure5.12e-10604
epiblast (generic)5.12e-10604
organ part7.40e-10219
posterior neural tube1.21e-0915
chordal neural plate1.21e-0915
segmental subdivision of nervous system2.14e-0813
organ2.30e-08511
segmental subdivision of hindbrain8.43e-0812
hindbrain8.43e-0812
presumptive hindbrain8.43e-0812
basal ganglion1.65e-079
nuclear complex of neuraxis1.65e-079
aggregate regional part of brain1.65e-079
collection of basal ganglia1.65e-079
cerebral subcortex1.65e-079
nucleus of brain2.35e-079
neural nucleus2.35e-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)

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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


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.