Data¶

cd snpsea
curl -LOk http://files.figshare.com/1504037/SNPsea_data_20140520.zip
unzip SNPsea_data_20140520.zip

Download the compressed archive with data required to perform this analysis (138M). The direct link to the zip shown above may be out of date and fail to load. If so, please visit the link below instead:

http://dx.doi.org/10.6084/m9.figshare.871430

Contents of the compressed archive with data:

Celiac_disease-Trynka2011-35_SNPs.gwas
HDL_cholesterol-Teslovich2010-46_SNPs.gwas
Multiple_sclerosis-IMSGC-51_SNPs.gwas
Red_blood_cell_count-Harst2012-45_SNPs.gwas

GeneAtlas2004.gct.gz  # Gene Atlas 2004 Affymetrix expression matrix
ImmGen2012.gct.gz     # ImmGen 2012 Affymetrix expression matrix
FANTOM2014.gct.gz     # FANTOM5 2014 CAGE matrix
GO2013.gct.gz         # Gene Ontology 2013 binary annotation matrix

NCBIgenes2013.bed.gz  # NCBI gene intervals
Lango2010.txt.gz      # LD-pruned SNPs
TGP2011.bed.gz        # 1000 Genomes Project SNP linkage intervals

SNP sets¶

Phenotype	SNPs	Loci	Reference
Celiac disease	35	34	Table 2 (Trynka, et al. 2011)
HDL cholesterol	46	46	Supp. Table 2 (Teslovich, et al. 2010)
Multiple sclerosis	51	47	Supp. Table A (IMSGC WTCCC 2011)
Red blood cell count	45	45	Table 1 (Harst et al. 2012)

Celiac_disease-Trynka2011-35_SNPs.gwas¶

35 SNPs associated with Celiac disease taken from Table 2. Positions are on hg19. All SNPs have \(P \le 5e-8\).

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.

HDL_cholesterol-Teslovich2010-46_SNPs.gwas¶

46 SNPs associated with HDL taken from Supplementary Table 2. Positions are on hg19. All SNPs have \(P \le 5e-8\).

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.

Multiple_sclerosis-IMSGC-51_SNPs.gwas¶

51 SNPs associated with Multiple Sclerosis taken from Supplementary Table A. Positions are on hg19. All SNPs have \(P \le 5e-8\).

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.

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 \(P \le 5e-8\).

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.

Gene matrices¶

Type	Genes	Conditions	Species	Reference
Affy	17581	79 tissues	homo sapiens	GeneAtlas 2004
Affy	15139	249 cells	mus musculus	ImmGen 2012
CAGE	18502	533 cells	homo sapiens	FANTOM5 2014
Binary	19111	1751 terms	homo sapiens, mus musculus	Gene Ontology 2013, Homologene

GeneAtlas2004.gct.gz¶

Gene expression data for 79 human tissues from GSE1133. We averaged the expression values for tissue replicates. For each gene, we selected the single probe with the largest minimum value. Finally, we converted the file to GCT format.

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.

GO2013.gct.gz¶

A GCT formatted gene matrix with 1,751 annotation terms (1s and 0s indicating presence or absence of the gene in a Gene Ontology term).

We downloaded the OBO file from Gene Ontology (data-version: 2013-06-29, CVS revision: 9700).

For each gene, we climbed the hierarchy of ontology terms and applied parental terms. If a gene is annotated with some term \(T\), we also add all of the terms that are parents of \(T\). We copy terms between homologous genes using Homologene data. If a mouse gene is annotated with some term and the human homolog is not, then we copy the term to the human gene. We discard all GO terms assigned to fewer than 100 or to more than 1000 genes. This leaves us with a matrix of 19,111 genes and 1,751 terms.

ImmGen2012.gct.gz¶

Gene expression data for 249 blood cell types from GSE15907. We averaged cell type replicates. For each gene, we selected the single probe with the largest minimum.

FANTOM2014.gct.gz¶

CAGE data for 533 human cell types from FANTOM5. We averaged cell type replicates. We discarded CAGE entries with 0 or multiple corresponding NCBI Entrez IDs. Then, we summed the CAGE entries for each gene.

LD-pruned SNPs and Genomic Intervals¶

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.

NCBIgenes2013.bed.gz¶

All human start and stop positions taken from:

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz

TGP2011.bed.gz¶

Linkage intervals for a filtered set of SNPs from the 1000 Genomes Project Phase 1 (May 21, 2011). We downloaded a filtered (diallelic and 5 or more copies of the minor allele) set of markers from the BEAGLE website and calculated pairwise LD (EUR) for all SNPs in a 1 Mb sliding window. The linkage intervals were extended to the nearest HapMap recombination hotspot with >3 cM/Mb recombination rate ( Supplementary Figure 1 ).