Limits...
VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes.

Burren OS, Guo H, Wallace C - Bioinformatics (2014)

Bottom Line: Genome-wide association studies (GWAS) have identified many loci implicated in disease susceptibility.Integration of GWAS summary statistics (P-values) and functional genomic datasets should help to elucidate mechanisms.The approach is implemented in VSEAMS, a freely available software pipeline.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genetics, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK and MRC Biostatistics Unit, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK.

Show MeSH

Related in: MedlinePlus

T1D susceptible SNP enrichment (excluding major histocompatibility complex (MHC)) within transcription factor perturbed gene sets from Cusanovich et al. (2014) SNPs are pruned on the basis of r2 threshold 0.95. A positive Z-score indicates enrichment, labels denote associated P-values. Black bars indicate that the knocked-down transcription factor overlaps a known autoimmune susceptibility locus curated in ImmunoBase
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4296156&req=5

btu571-F4: T1D susceptible SNP enrichment (excluding major histocompatibility complex (MHC)) within transcription factor perturbed gene sets from Cusanovich et al. (2014) SNPs are pruned on the basis of r2 threshold 0.95. A positive Z-score indicates enrichment, labels denote associated P-values. Black bars indicate that the knocked-down transcription factor overlaps a known autoimmune susceptibility locus curated in ImmunoBase

Mentions: Genes perturbed by 3 of 59 transcription factors in knock-down experiments (Cusanovich et al., 2014) were enriched for association with T1D (Fig. 4): IKZF3 (P = 1.1 × ), BATF (P = 4.4 × ) and ESRRA (P = 8.0 × ), where n is the number of genes in each set. Fourteen genes are common to all three sets (Supplementary Fig. S1 and Supplementary Table S2).Fig. 4.


VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes.

Burren OS, Guo H, Wallace C - Bioinformatics (2014)

T1D susceptible SNP enrichment (excluding major histocompatibility complex (MHC)) within transcription factor perturbed gene sets from Cusanovich et al. (2014) SNPs are pruned on the basis of r2 threshold 0.95. A positive Z-score indicates enrichment, labels denote associated P-values. Black bars indicate that the knocked-down transcription factor overlaps a known autoimmune susceptibility locus curated in ImmunoBase
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4296156&req=5

btu571-F4: T1D susceptible SNP enrichment (excluding major histocompatibility complex (MHC)) within transcription factor perturbed gene sets from Cusanovich et al. (2014) SNPs are pruned on the basis of r2 threshold 0.95. A positive Z-score indicates enrichment, labels denote associated P-values. Black bars indicate that the knocked-down transcription factor overlaps a known autoimmune susceptibility locus curated in ImmunoBase
Mentions: Genes perturbed by 3 of 59 transcription factors in knock-down experiments (Cusanovich et al., 2014) were enriched for association with T1D (Fig. 4): IKZF3 (P = 1.1 × ), BATF (P = 4.4 × ) and ESRRA (P = 8.0 × ), where n is the number of genes in each set. Fourteen genes are common to all three sets (Supplementary Fig. S1 and Supplementary Table S2).Fig. 4.

Bottom Line: Genome-wide association studies (GWAS) have identified many loci implicated in disease susceptibility.Integration of GWAS summary statistics (P-values) and functional genomic datasets should help to elucidate mechanisms.The approach is implemented in VSEAMS, a freely available software pipeline.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genetics, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK and MRC Biostatistics Unit, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK.

Show MeSH
Related in: MedlinePlus