GSA-SNP2

"Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10),  e60(2018), Sora Yoon, Hai C T Nguyen, Yun J Yoo, Jinhwan Kim, Bukyung Baik, Sounkou Kim, Jin Kim, Sangsoo Kim, Dougu Nam.

• PubMed ID: 29562348 ( https://www.ncbi.nlm.nih.gov/pubmed/29562348 )

• NAR DOI: 10.1093/nar/gky175 ( https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky175/4942469 )

• Project website: https://sites.google.com/view/gsasnp2

Test package includes:

• A Windows GUI version with a friendly graphical user interface, SNP mapping data (GRCh37(hg19), padding 20,000), genotype correlation (European) and sample data (DIAGRAM) for an immediate test. Choose GRCh37(hg19) and MSigDB for testing DIAGRAM data, and obtain the following result: DIAGRAM_result. Pathways described in the 16 curated T2D related pathways (Morris et al. Nat. Gen. 2012) are marked yellow (q-value<= 0.25)

• A Windows command-line version with a ready executable script (run_gsasnp2.bat). Tested on Windows XP, Windows 10.

• A Linux command-line version with a ready executable scritp (run_gsasnp2.sh). Tested on Ubuntu 16.04, CentOS 7.

• A MacOS command-line version with a ready executable script (run_gsasnp2.sh). Tested on MacOSX 10.11 (El Capitan), MacOSX 10.12 (Sierra).

Comparison with other competitive methods

• Performance of GSA-SNP2 was compared with those of five existing competitive methods, GSA-SNP, iGSEA4GWAS MAGENTA, INRICH and GOWINDA. GSA-SNP2 exhibited greatly improved type I error control compared to GSA-SNP, but was still a little liberal compared to the other tools.

• DIAGRAM consortium GWAS p-values (European) were used to compare the statistical power. 16 curated T2D related pathways (Morris et al. Nat. Genetics 2012) as well as the terms including ‘diabetes’ were regarded as true positives (TPs). GSA-SNP2 exhibited high power and best ranks of TPs. See the results here.

DATA DESCRIPTION

'home' directory

• 170329_gsasnp2_manual.pdf: A detailed manual for both Windows and Linux versions of the software.

• test-package.zip (~390 MB): Test package including the ALL versions of the program (Windows-GUI, Windows-CMD, MacOSX-CMD) and executable scripts, SNP mapping data (GRCh37(hg19), padding 20,000), genotype correlation (European) and sample data (DIAGRAM) for an immediate test. Choose hg19 and MSigDB for testing the DIAGRAM data.

• gsasnp2-windows-gui.zip (~4 MB): Windows version with graphic user interface (program only).

• gsasnp2-windows-cmd.zip (~3 MB): Windows command-line version (program only).

• gsasnp2-mac-cmd.zip (~1 MB) MacOS command-line version (program only).

• gsasnp2-linux-cmd.zip (~3 MB): Linux command-line version (program only).

• test-sample-data.zip (~379 MB): Test sample data for testing the Linux command-line version.

'data' directory

• data/gene-map/__: SNP-Gene mapping data with various padding ranges for three genome versions: GRCh36(hg18), GRCh37(hg19), and GRCh38(hg38).

• data/adjacent-gene-correlation.zip: Full generated data of inter-gene genotype correlations for five races: American, African, East Asian, European, South Asian.

• data/snp-location-data.zip: SNP location information for the different versions of gene map.

• data/gene-id-symbol-conversion.zip: Gene ID conversion mapping table: Ensembl, Entrezgene and Uniprot_swissprot gene (protein) IDs are converted to gene symbols.

• data/popular-pathway-list.zip: Some of the popularly used human pathway gene-sets.

• data/network-data.zip: Protein interaction network data (STRING database and HIPPIE database as of summer 2016).