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24 Kirov et al.1. Retrieve the gene set uploaded in Subheading 3.1.1. To do so login to WebGestalt,select “lymph node” from the pull-down menu next to RETRIEVE button andpress RETRIEVE.2. Press the GET ORTHOLOGS button. In this case the button wouldread “get mouse orthologs,” because the starting gene set is human.3. Press SAVE in the new window that opens and follow the normal gene setdescription step.3.1.2.2. BOOLEAN OPERATIONS: UNIONS, INTERSECTIONS, AND DIFFERENCESComparing the composition of different gene sets is important in order tocompare genes’ behavior under different conditions. In this case the overlap ofgene sets enriched in cerebellum vs cerebrum will be compared.Create the intersection of gene set “cerebellum” (A) and gene set “cerebrum”(B):1. Login to WebGestalt. Unless gene sets “cerebellum” or “cerebrum” have beenuploaded previously, upload them at this point. This will make both sets availablefrom the pull-down menus next to BOOLEAN OPERATIONS button.2. Select gene set A (cerebrum) and B (cerebellum).3. Select intersection and press BOOLEAN OPERATIONS to create the new gene set.4. Press SAVE and enter the new set name and description.3.1.2.3. BOOLEAN OPERATIONS FOR SETS FROM DIFFERENT SPECIES1. Upload organism 1 gene set (set A) following the method in Subheading 3.1.2.1.2. Upload organism 2 gene set (set B) following the method in Subheading 3.1.2.1.3. Using set A follow steps 1–3 as described in Subheading 3.1.2.1., which willcreate gene set AB.4. Create set BA as in step 3, using set B instead of A.5. Check if sets AB and BA have the same number of genes.3.2. Information RetrievalThe following data can be currently collected in WebGestalt: gene IDs/accessionnumbers (EntrezGene, RefSeq, UniGene, UniProt, and Ensembl gene stableid), gene names and symbols, cytogenetic and physical mapping data, proteindomains, Online Mendelian Inheritance in Man (OMIM), genome reference intofunction, publications, GO, KEGG, Biocarta, and phenotype.1. Check the checkboxes denoting the type of data one needs.2. Press the “Information retrieval” button and save the results (and remember thelocation of the file). Some browsers are configured to automatically open theresults through an Excel plugin (this behavior can be changed through thebrowser “Helper application” preferences or the operating system (OS) foldersettings).