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SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci

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Version 4 2014-05-20, 21:19
Version 3 2014-05-20, 21:19
Version 2 2014-02-13, 03:09
Version 1 2013-12-08, 05:51
dataset
posted on 2014-05-20, 21:19 authored by Kamil SlowikowskiKamil Slowikowski, Xinli Hu, Soumya Raychaudhuri

Updated May 20, 2014.

 

This archive contains data for:

Slowikowski, et al. SNPsea: an algorithm to identify cell types, tissues, and pathways that affect risk loci. Bioinformatics (2014). doi:10.1093/bioinformatics/btu326

 

Please see the SNPsea documentation for more details:

http://snpsea.readthedocs.org/en/latest/data.html

 

CONTENTS

 

GWAS SNPs on hg19 with P <= 5-e8 extracted from tables in pdfs.

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 gene expression matrix (Affymetrix)

ImmGen2012.gct.gz
- ImmGen 2012 gene expression matrix (Affymetrix)

FANTOM2014.gct.gz
- RIKEN FANTOM5 gene expression matrix (CAGE)

GO2013.gct.gz
- Gene Ontology 2013 gene annotation matrix (binary annotations)


NCBIgenes2013.bed.gz
- Homo sapiens NCBI gene intervals

Lango2010.txt.gz
- LD-pruned SNPs

TGP2011.bed.gz
- 1000 Genomes Project SNP linkage disequilibrium (LD) intervals

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