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Coexpression cluster:C749: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!2.25e-19!143;UBERON:0000486!1.25e-16!82;UBERON:0000914!4.34e-16!83;UBERON:0002329!4.34e-16!83;UBERON:0003077!4.34e-16!83;UBERON:0003059!4.34e-16!83;UBERON:0007282!4.34e-16!83;UBERON:0009618!4.34e-16!83;UBERON:0007285!4.34e-16!83;UBERON:0000119!7.45e-16!312;UBERON:0002100!8.37e-16!216;UBERON:0000490!1.61e-15!138;UBERON:0000483!6.78e-15!309;UBERON:0000475!1.50e-14!365;UBERON:0003914!4.68e-14!118;UBERON:0000481!6.80e-14!347;UBERON:0003104!8.79e-14!238;UBERON:0009142!8.79e-14!238;UBERON:0004290!1.46e-13!70;UBERON:0002049!1.08e-12!79;UBERON:0007798!1.08e-12!79;UBERON:0000468!2.33e-11!659;UBERON:0001134!3.29e-11!61;UBERON:0002036!3.29e-11!61;UBERON:0003082!3.29e-11!61;UBERON:0002385!1.43e-10!63;UBERON:0001015!1.43e-10!63;UBERON:0000383!1.43e-10!63;UBERON:0000922!7.17e-10!612;UBERON:0003102!1.45e-09!95;UBERON:0001981!3.52e-09!60;UBERON:0007500!3.52e-09!60;UBERON:0004537!3.52e-09!60;UBERON:0006965!3.52e-09!60;UBERON:0001444!5.11e-09!48;UBERON:0000055!7.57e-09!69;UBERON:0000467!8.43e-09!625;UBERON:0000480!1.39e-08!626;UBERON:0001637!1.75e-08!42;UBERON:0003509!1.75e-08!42;UBERON:0004572!1.75e-08!42;UBERON:0002050!2.00e-08!605;UBERON:0005423!2.00e-08!605;UBERON:0000923!2.03e-08!604;UBERON:0005291!2.03e-08!604;UBERON:0006598!2.03e-08!604;UBERON:0002532!2.03e-08!604;UBERON:0004872!2.57e-08!84;UBERON:0005085!4.81e-08!29;UBERON:0000019!7.10e-08!19;UBERON:0000047!7.10e-08!19;UBERON:0004088!7.10e-08!19;UBERON:0003072!7.10e-08!19;UBERON:0003071!7.10e-08!19;UBERON:0004128!7.10e-08!19;UBERON:0000970!2.20e-07!20;UBERON:0004535!4.37e-07!110;UBERON:0001456!5.38e-07!21
|ontology_enrichment_uberon=UBERON:0005256!2.25e-19!143;UBERON:0000486!1.25e-16!82;UBERON:0000914!4.34e-16!83;UBERON:0002329!4.34e-16!83;UBERON:0003077!4.34e-16!83;UBERON:0003059!4.34e-16!83;UBERON:0007282!4.34e-16!83;UBERON:0009618!4.34e-16!83;UBERON:0007285!4.34e-16!83;UBERON:0000119!7.45e-16!312;UBERON:0002100!8.37e-16!216;UBERON:0000490!1.61e-15!138;UBERON:0000483!6.78e-15!309;UBERON:0000475!1.50e-14!365;UBERON:0003914!4.68e-14!118;UBERON:0000481!6.80e-14!347;UBERON:0003104!8.79e-14!238;UBERON:0009142!8.79e-14!238;UBERON:0004290!1.46e-13!70;UBERON:0002049!1.08e-12!79;UBERON:0007798!1.08e-12!79;UBERON:0000468!2.33e-11!659;UBERON:0001134!3.29e-11!61;UBERON:0002036!3.29e-11!61;UBERON:0003082!3.29e-11!61;UBERON:0002385!1.43e-10!63;UBERON:0001015!1.43e-10!63;UBERON:0000383!1.43e-10!63;UBERON:0000922!7.17e-10!612;UBERON:0003102!1.45e-09!95;UBERON:0001981!3.52e-09!60;UBERON:0007500!3.52e-09!60;UBERON:0004537!3.52e-09!60;UBERON:0006965!3.52e-09!60;UBERON:0001444!5.11e-09!48;UBERON:0000055!7.57e-09!69;UBERON:0000467!8.43e-09!625;UBERON:0000480!1.39e-08!626;UBERON:0001637!1.75e-08!42;UBERON:0003509!1.75e-08!42;UBERON:0004572!1.75e-08!42;UBERON:0002050!2.00e-08!605;UBERON:0005423!2.00e-08!605;UBERON:0000923!2.03e-08!604;UBERON:0005291!2.03e-08!604;UBERON:0006598!2.03e-08!604;UBERON:0002532!2.03e-08!604;UBERON:0004872!2.57e-08!84;UBERON:0005085!4.81e-08!29;UBERON:0000019!7.10e-08!19;UBERON:0000047!7.10e-08!19;UBERON:0004088!7.10e-08!19;UBERON:0003072!7.10e-08!19;UBERON:0003071!7.10e-08!19;UBERON:0004128!7.10e-08!19;UBERON:0000970!2.20e-07!20;UBERON:0004535!4.37e-07!110;UBERON:0001456!5.38e-07!21
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}}
}}

Revision as of 20:46, 8 August 2012


Full id: C749_Wilms_rhabdomyosarcoma_medulloblastoma_fibrous_retinoblastoma_endometrial_schwannoma



Phase1 CAGE Peaks

Hg19::chr12:66218152..66218174,+p10@HMGA2
Hg19::chr12:66218183..66218209,+p4@HMGA2
Hg19::chr12:66218212..66218244,+p5@HMGA2
Hg19::chr12:66218255..66218304,+p3@HMGA2
Hg19::chr12:66218378..66218401,+p6@HMGA2
Hg19::chr12:66218413..66218418,+p17@HMGA2
Hg19::chr12:66218420..66218439,+p12@HMGA2
Hg19::chr12:66218443..66218461,+p8@HMGA2
Hg19::chr12:66218469..66218477,+p16@HMGA2
Hg19::chr12:66218573..66218596,+p7@HMGA2
Hg19::chr12:66218598..66218645,+p2@HMGA2


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><br>

Uber Anatomy
Ontology termp-valuen
trunk mesenchyme2.25e-19143
multilaminar epithelium1.25e-1682
somite4.34e-1683
paraxial mesoderm4.34e-1683
presomitic mesoderm4.34e-1683
presumptive segmental plate4.34e-1683
trunk paraxial mesoderm4.34e-1683
presumptive paraxial mesoderm4.34e-1683
cell layer7.45e-16312
trunk8.37e-16216
unilaminar epithelium1.61e-15138
epithelium6.78e-15309
organism subdivision1.50e-14365
epithelial tube4.68e-14118
multi-tissue structure6.80e-14347
mesenchyme8.79e-14238
entire embryonic mesenchyme8.79e-14238
dermomyotome1.46e-1370
vasculature1.08e-1279
vascular system1.08e-1279
multi-cellular organism2.33e-11659
skeletal muscle tissue3.29e-1161
striated muscle tissue3.29e-1161
myotome3.29e-1161
muscle tissue1.43e-1063
musculature1.43e-1063
musculature of body1.43e-1063
embryo7.17e-10612
surface structure1.45e-0995
blood vessel3.52e-0960
epithelial tube open at both ends3.52e-0960
blood vasculature3.52e-0960
vascular cord3.52e-0960
subdivision of head5.11e-0948
vessel7.57e-0969
anatomical system8.43e-09625
anatomical group1.39e-08626
artery1.75e-0842
arterial blood vessel1.75e-0842
arterial system1.75e-0842
embryonic structure2.00e-08605
developing anatomical structure2.00e-08605
germ layer2.03e-08604
embryonic tissue2.03e-08604
presumptive structure2.03e-08604
epiblast (generic)2.03e-08604
splanchnic layer of lateral plate mesoderm2.57e-0884
ectodermal placode4.81e-0829
camera-type eye7.10e-0819
simple eye7.10e-0819
ocular region7.10e-0819
optic cup7.10e-0819
eye primordium7.10e-0819
optic vesicle7.10e-0819
eye2.20e-0720
cardiovascular system4.37e-07110
face5.38e-0721


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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