SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci
Year: 2013
Type: dataset
Abstract: February 12, 2014 This archive contains data for: SNPsea: an algorithm to identify cell types, tissues, and pathways that affect risk loci Please see the SNPsea documentation for more details: http://www.broadinstitute.org/mpg/snpsea Celiac_disease-Trynka2011-35_SNPs.gwas 35 SNPs associated with Celiac disease taken from Table 2. Positions are on hg19. All SNPs have P <= 5e-8. doi:10.1038/ng.998 PMID: 22057235 Trynka G, Hunt KA, Bockett NA, et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet. 2011;43(12):1193-201. http://www.ncbi.nlm.nih.gov/pubmed/22057235 HDL_cholesterol-Tesolvich2010-46_SNPs.gwas 46 SNPs associated with HDL taken from Supplementary Table 2. Positions are on hg19. All SNPs have P <= 5e-8. doi:10.1038/nature09270 PMID: 20686565 Teslovich TM, Musunuru K, Smith AV, et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature. 2010;466(7307):707-13. http://www.ncbi.nlm.nih.gov/pubmed/20686565 Multiple_sclerosis-IMSGC-51_SNPs.gwas 51 SNPs associated with Multiple Sclerosis taken from Supplementary Table A. Positions are on hg19. All SNPs have P <= 5e-8. doi:10.1038/nature10251 PMID: 21833088 Sawcer S, Hellenthal G, Pirinen M, et al. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature. 2011;476(7359):214-9. http://www.ncbi.nlm.nih.gov/pubmed/21833088 Red_blood_cell_count-Harst2012-45_SNPs.gwas 45 SNPs associated with red blood cell count (RBC) taken from Table 1. Positions are on hg19. All SNPs have P <= 5e-8. doi:10.1038/nature11677 PMID: 23222517 Van der harst P, Zhang W, Mateo leach I, et al. Seventy-five genetic loci influencing the human red blood cell. Nature. 2012;492(7429):369-75. http://www.ncbi.nlm.nih.gov/pubmed/23222517 - - - GeneAtlas2004.gct.gz Gene expression data for 79 human tissues from GSE1133. Replicates for each tissue profile were averaged. For each gene, the single probe with the largest minimum was selected. Su AI et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A, 2004 Apr 9;101(16):6062-7 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1133 GO2013.gct.gz A GCT formatted gene matrix with 1s and 0s indicating presence or absence of genes in Gene Ontology annotations. http://www.geneontology.org/ ImmGen2012.gct.gz Gene expression data for 249 blood cell types from GSE15907. Replicates for each cell type profile were averaged. For each gene, the single probe with the largest minimum was selected. Immunological Genome Project http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907 - - - NCBIgenes2013.bed.gz All human gene start and stop positions taken from: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz Lango2010.txt.gz A list of SNPs that span the whole genome, pruned by linkage disequilibrium (LD). SNPsea samples null SNP sets matched on the number of genes in the user's SNP set from this list. See this paper for more information: Lango allen H, Estrada K, Lettre G, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010;467(7317):832-8. http://www.ncbi.nlm.nih.gov/pubmed/20881960 TGP2011.bed.gz Linkage intervals for a filtered set of SNPs from the 1000 Genomes Project Phase 1 (May 21, 2011). SNP genotypes were obtained from the BEAGLE release v3 website and processed to create linkage intervals for each SNP. The linkage intervals were extended to the nearest HapMap recombination hotspot with >3 cM/Mb recombination rate. http://www.1000genomes.org/ http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/ http://hapmap.ncbi.nlm.nih.gov/downloads/
Source: Figshare
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4394514562