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Coexpression cluster:C3026: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.91e-43!115;UBERON:0005743!8.32e-32!86;UBERON:0001049!2.61e-31!57;UBERON:0005068!2.61e-31!57;UBERON:0006241!2.61e-31!57;UBERON:0007135!2.61e-31!57;UBERON:0001017!4.58e-31!82;UBERON:0000073!2.40e-29!94;UBERON:0001016!2.40e-29!94;UBERON:0000955!2.66e-27!69;UBERON:0006238!2.66e-27!69;UBERON:0002616!1.70e-26!59;UBERON:0003080!1.81e-23!42;UBERON:0003075!1.81e-23!86;UBERON:0007284!1.81e-23!86;UBERON:0002780!8.73e-23!41;UBERON:0001890!8.73e-23!41;UBERON:0006240!8.73e-23!41;UBERON:0004121!1.17e-22!169;UBERON:0002346!1.98e-22!90;UBERON:0000924!3.73e-22!173;UBERON:0006601!3.73e-22!173;UBERON:0000033!5.16e-22!123;UBERON:0000153!2.05e-21!129;UBERON:0007811!2.05e-21!129;UBERON:0002020!3.64e-19!34;UBERON:0003528!3.64e-19!34;UBERON:0001893!5.13e-19!34;UBERON:0002791!1.80e-18!33;UBERON:0000475!1.13e-17!365;UBERON:0001869!1.22e-17!32;UBERON:0003056!5.59e-16!61;UBERON:0000481!1.24e-14!347;UBERON:0000956!6.38e-14!25;UBERON:0000203!6.38e-14!25;UBERON:0000477!3.69e-13!286;UBERON:0002619!7.13e-13!22;UBERON:0000062!1.76e-12!511;UBERON:0004111!4.24e-12!241;UBERON:0001950!1.25e-11!20;UBERON:0000025!2.80e-10!194;UBERON:0000468!1.33e-09!659;UBERON:0000467!2.24e-09!625;UBERON:0000480!3.58e-09!626;UBERON:0003076!6.43e-09!15;UBERON:0003057!6.43e-09!15;UBERON:0000922!2.09e-08!612;UBERON:0000483!2.30e-08!309;UBERON:0002050!2.87e-08!605;UBERON:0005423!2.87e-08!605;UBERON:0000119!3.19e-08!312;UBERON:0000923!4.50e-08!604;UBERON:0005291!4.50e-08!604;UBERON:0006598!4.50e-08!604;UBERON:0002532!4.50e-08!604;UBERON:0004732!1.36e-07!13;UBERON:0000064!2.56e-07!219;UBERON:0002298!4.25e-07!8;UBERON:0004733!6.34e-07!12;UBERON:0002028!6.34e-07!12;UBERON:0007277!6.34e-07!12;UBERON:0002308!9.58e-07!9;UBERON:0000125!9.58e-07!9
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}}
}}

Revision as of 18:50, 8 August 2012


Full id: C3026_medulla_aorta_optic_spinal_locus_corpus_skeletal



Phase1 CAGE Peaks

Hg19::chr10:5454633..5454661,+p4@NET1
Hg19::chr10:5454672..5454689,+p1@CU690984
Hg19::chr4:79892654..79892672,+p5@LOC100505875


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:0005089Rho guanyl-nucleotide exchange factor activity0.0288031319910514
GO:0035023regulation of Rho protein signal transduction0.0288031319910514
GO:0001558regulation of cell growth0.0288031319910514
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0288031319910514
GO:0007266Rho protein signal transduction0.0288031319910514
GO:0016049cell growth0.0288031319910514
GO:0040008regulation of growth0.0288031319910514
GO:0008361regulation of cell size0.0288031319910514
GO:0005085guanyl-nucleotide exchange factor activity0.0356450410141685
GO:0046578regulation of Ras protein signal transduction0.0356450410141685
GO:0007265Ras protein signal transduction0.0356450410141685
GO:0005083small GTPase regulator activity0.0356450410141685
GO:0051056regulation of small GTPase mediated signal transduction0.0356450410141685
GO:0032989cellular structure morphogenesis0.0356450410141685
GO:0000902cell morphogenesis0.0356450410141685
GO:0030695GTPase regulator activity0.0489373601789709



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 organism5.91e-43115
neural tube2.61e-3157
neural rod2.61e-3157
future spinal cord2.61e-3157
neural keel2.61e-3157
central nervous system4.58e-3182
regional part of nervous system2.40e-2994
nervous system2.40e-2994
brain2.66e-2769
future brain2.66e-2769
regional part of brain1.70e-2659
anterior neural tube1.81e-2342
neural plate1.81e-2386
presumptive neural plate1.81e-2386
regional part of forebrain8.73e-2341
forebrain8.73e-2341
future forebrain8.73e-2341
ectoderm-derived structure1.17e-22169
neurectoderm1.98e-2290
ectoderm3.73e-22173
presumptive ectoderm3.73e-22173
head5.16e-22123
anterior region of body2.05e-21129
craniocervical region2.05e-21129
gray matter3.64e-1934
brain grey matter3.64e-1934
telencephalon5.13e-1934
regional part of telencephalon1.80e-1833
organism subdivision1.13e-17365
cerebral hemisphere1.22e-1732
pre-chordal neural plate5.59e-1661
multi-tissue structure1.24e-14347
cerebral cortex6.38e-1425
pallium6.38e-1425
anatomical cluster3.69e-13286
regional part of cerebral cortex7.13e-1322
organ1.76e-12511
anatomical conduit4.24e-12241
neocortex1.25e-1120
tube2.80e-10194
multi-cellular organism1.33e-09659
anatomical system2.24e-09625
anatomical group3.58e-09626
posterior neural tube6.43e-0915
chordal neural plate6.43e-0915
embryo2.09e-08612
epithelium2.30e-08309
embryonic structure2.87e-08605
developing anatomical structure2.87e-08605
cell layer3.19e-08312
germ layer4.50e-08604
embryonic tissue4.50e-08604
presumptive structure4.50e-08604
epiblast (generic)4.50e-08604
segmental subdivision of nervous system1.36e-0713
organ part2.56e-07219
brainstem4.25e-078
segmental subdivision of hindbrain6.34e-0712
hindbrain6.34e-0712
presumptive hindbrain6.34e-0712
nucleus of brain9.58e-079
neural nucleus9.58e-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.