ATC The Anatomical Therapeutic Chemical (ATC) Classification System is used for the classification of active ingredients of drugs according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. This will be used as background genes.Īll the genes targeted by the drugs in the database If you want to know the drug names targeting your genes, set this flag (without any arguments after that).Ī list of all genes in the scope of your analysis if available. Input your list of genes as a text file with one column.Ĭhoose from ATC or ICD for a drug indication categorization system. To make a gene set, define P value threshold of your choice, and make a text file with a set of genes which pass that threshold using the output from the above softwares. Reimplementation in python for the conversion is distributed here. If your would like to perform post-GWAS analysis, and if you would like to convert SNP-level statisitcs to gene-level ones, here are some of the options. example/RA_trans.genes can be used as genes identified in RA meta-analysis by Okada et al ( Nature 2014).įYI: How can I define a gene set from GWAS sumstats? example/megastroke.genes can be used as genes identified by MEGASTROKE consortium ( Nat Genet 2018). example/ directory for example gene sets. Make a text file with one column, which contains genes by HGNC gene symbol. example/megastroke.genes -out my_GREP_test -test ATC -output-drug-name Prepare your input
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