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Coexpression cluster:C2112: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!8.16e-08!14
|ontology_enrichment_disease=DOID:2394!8.16e-08!14
|ontology_enrichment_uberon=UBERON:0000475!2.95e-26!365;UBERON:0000914!1.71e-23!83;UBERON:0002329!1.71e-23!83;UBERON:0003077!1.71e-23!83;UBERON:0003059!1.71e-23!83;UBERON:0007282!1.71e-23!83;UBERON:0009618!1.71e-23!83;UBERON:0007285!1.71e-23!83;UBERON:0000119!8.55e-23!312;UBERON:0000483!5.90e-22!309;UBERON:0000486!2.42e-20!82;UBERON:0000481!1.75e-18!347;UBERON:0004290!1.99e-18!70;UBERON:0001134!5.74e-16!61;UBERON:0002036!5.74e-16!61;UBERON:0003082!5.74e-16!61;UBERON:0002385!1.01e-15!63;UBERON:0001015!1.01e-15!63;UBERON:0000383!1.01e-15!63;UBERON:0000033!1.59e-15!123;UBERON:0005256!6.40e-15!143;UBERON:0000468!7.78e-15!659;UBERON:0000153!1.03e-14!129;UBERON:0007811!1.03e-14!129;UBERON:0000924!1.05e-14!173;UBERON:0006601!1.05e-14!173;UBERON:0004121!4.07e-14!169;UBERON:0000467!6.15e-14!625;UBERON:0000480!1.01e-13!626;UBERON:0000477!2.98e-13!286;UBERON:0001637!1.48e-12!42;UBERON:0003509!1.48e-12!42;UBERON:0004572!1.48e-12!42;UBERON:0004872!1.58e-12!84;UBERON:0004111!5.70e-12!241;UBERON:0000025!1.32e-11!194;UBERON:0002049!2.19e-11!79;UBERON:0007798!2.19e-11!79;UBERON:0001981!3.71e-11!60;UBERON:0007500!3.71e-11!60;UBERON:0004537!3.71e-11!60;UBERON:0006965!3.71e-11!60;UBERON:0000922!8.33e-11!612;UBERON:0003102!1.10e-10!95;UBERON:0002050!1.24e-10!605;UBERON:0005423!1.24e-10!605;UBERON:0000923!1.46e-10!604;UBERON:0005291!1.46e-10!604;UBERON:0006598!1.46e-10!604;UBERON:0002532!1.46e-10!604;UBERON:0004573!5.39e-10!33;UBERON:0004571!5.39e-10!33;UBERON:0002346!9.09e-10!90;UBERON:0000055!3.02e-09!69;UBERON:0003075!3.09e-09!86;UBERON:0007284!3.09e-09!86;UBERON:0000955!3.97e-09!69;UBERON:0006238!3.97e-09!69;UBERON:0002616!5.08e-09!59;UBERON:0002097!1.25e-08!40;UBERON:0005743!2.77e-08!86;UBERON:0001017!3.43e-08!82;UBERON:0000479!4.05e-08!787;UBERON:0001049!5.05e-08!57;UBERON:0005068!5.05e-08!57;UBERON:0006241!5.05e-08!57;UBERON:0007135!5.05e-08!57;UBERON:0002199!5.49e-08!45;UBERON:0002416!5.49e-08!45;UBERON:0000064!6.75e-08!219;UBERON:0002100!7.48e-08!216;UBERON:0003914!7.61e-08!118;UBERON:0000073!7.72e-08!94;UBERON:0001016!7.72e-08!94;UBERON:0004535!7.95e-08!110;UBERON:0000490!1.00e-07!138;UBERON:0001009!1.34e-07!113;UBERON:0001869!1.46e-07!32;UBERON:0003056!1.67e-07!61;UBERON:0001893!1.96e-07!34;UBERON:0000956!2.34e-07!25;UBERON:0000203!2.34e-07!25;UBERON:0002020!3.35e-07!34;UBERON:0003528!3.35e-07!34;UBERON:0002791!4.25e-07!33;UBERON:0002619!7.58e-07!22;UBERON:0003129!7.67e-07!11;UBERON:0001950!8.31e-07!20
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}}
}}

Revision as of 18:00, 8 August 2012


Full id: C2112_Smooth_Amniotic_mesenchymal_Myoblast_Fibroblast_Lens_cerebellum



Phase1 CAGE Peaks

Hg19::chr11:131781197..131781214,+p14@NTM
Hg19::chr11:131781224..131781254,+p5@NTM
Hg19::chr11:131781256..131781281,+p11@NTM
Hg19::chr11:131781290..131781355,+p2@NTM


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

No GOStat results

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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
organism subdivision2.95e-26365
somite1.71e-2383
paraxial mesoderm1.71e-2383
presomitic mesoderm1.71e-2383
presumptive segmental plate1.71e-2383
trunk paraxial mesoderm1.71e-2383
presumptive paraxial mesoderm1.71e-2383
cell layer8.55e-23312
epithelium5.90e-22309
multilaminar epithelium2.42e-2082
multi-tissue structure1.75e-18347
dermomyotome1.99e-1870
skeletal muscle tissue5.74e-1661
striated muscle tissue5.74e-1661
myotome5.74e-1661
muscle tissue1.01e-1563
musculature1.01e-1563
musculature of body1.01e-1563
head1.59e-15123
trunk mesenchyme6.40e-15143
multi-cellular organism7.78e-15659
anterior region of body1.03e-14129
craniocervical region1.03e-14129
ectoderm1.05e-14173
presumptive ectoderm1.05e-14173
ectoderm-derived structure4.07e-14169
anatomical system6.15e-14625
anatomical group1.01e-13626
anatomical cluster2.98e-13286
artery1.48e-1242
arterial blood vessel1.48e-1242
arterial system1.48e-1242
splanchnic layer of lateral plate mesoderm1.58e-1284
anatomical conduit5.70e-12241
tube1.32e-11194
vasculature2.19e-1179
vascular system2.19e-1179
blood vessel3.71e-1160
epithelial tube open at both ends3.71e-1160
blood vasculature3.71e-1160
vascular cord3.71e-1160
embryo8.33e-11612
surface structure1.10e-1095
embryonic structure1.24e-10605
developing anatomical structure1.24e-10605
germ layer1.46e-10604
embryonic tissue1.46e-10604
presumptive structure1.46e-10604
epiblast (generic)1.46e-10604
systemic artery5.39e-1033
systemic arterial system5.39e-1033
neurectoderm9.09e-1090
vessel3.02e-0969
neural plate3.09e-0986
presumptive neural plate3.09e-0986
brain3.97e-0969
future brain3.97e-0969
regional part of brain5.08e-0959
skin of body1.25e-0840
central nervous system3.43e-0882
tissue4.05e-08787
neural tube5.05e-0857
neural rod5.05e-0857
future spinal cord5.05e-0857
neural keel5.05e-0857
integument5.49e-0845
integumental system5.49e-0845
organ part6.75e-08219
trunk7.48e-08216
epithelial tube7.61e-08118
regional part of nervous system7.72e-0894
nervous system7.72e-0894
cardiovascular system7.95e-08110
unilaminar epithelium1.00e-07138
circulatory system1.34e-07113
cerebral hemisphere1.46e-0732
pre-chordal neural plate1.67e-0761
telencephalon1.96e-0734
cerebral cortex2.34e-0725
pallium2.34e-0725
gray matter3.35e-0734
brain grey matter3.35e-0734
regional part of telencephalon4.25e-0733

Disease
Ontology termp-valuen


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.

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