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Association Analysis for Large-Scale Gene Set Data 23(17). Swissprot ID and Ensembl gene stable ID are also recommended as asecond option.Depending on the technical skills of the user, conversion choices wouldvary. Installing a local copy of the Ensembl MART database (18), BioMART(http://www.biomart.org/), or GeneKeyDB (19) locally, and directly queryingthe database might be the best choice, but will be much more challenging thanusing web-based tools, such as EnsMART, WebGestalt, and GSB (20). BothWebGestalt and GSB provide data set management modules, but GSB has bettergene set management functionality. It allows gene set sharing, comment addition,and set synchronization. WebGestalt has analysis modules and a slightly largerchoice of chip IDs. WebGestalt uses GeneKeyDB (21) to find the relevant data,whereas GSB is based on Ensembl. Several tools listed in Table 1, such asPANTHER and DAVID, also have integrated gene set conversion and managementfunctionality. If advanced gene set management is important, then eitherGSB or WebGestalt would be the appropriate choice for this step. OnlyWebGestalt is described herein whereas an overview for other tools exists athttp://bioinfo.vanderbilt.edu/mpaper/tc.html.1. Register in WebGestalt. This is necessary both to protect and store each users’gene sets. Storage is temporary. Gene sets are erased following each databaseupdate, but users are warned by email at least a week before the gene sets areremoved. The updates usually occur at 30–60 d periods.2. Prepare a text file (e.g., in notepad if Windows is used, TextWrangler [BareBones Software, Bedford, MA] for MacOS, and Emacs in *nix/Mac OS) withone identifier per line. Do not include a header row. If Microsoft Word is usedmake sure that in the “Save as type” field one chooses “Plain text.” As an alternativeone can use the example gene sets (see Subheading 2.). The descriptionfollowing is based on the example files.3. Access the gene set uploading/conversion form by selecting “Form file.” Fill inthe form and press the UPLOAD button. At this point the data set is stored in thedatabase and can be retrieved at a later time (see Note 4 on data set storage).4. Check for possible inaccuracies, for example:• The gene list size in the file should be the same or bigger (in case some genesare not in the supporting database) than the one reported by the conversion tool(see Notes 2 and 3 for explanation).• If the number of genes is far smaller than the input, there might be a problemin the upload process.3.1.2. Gene Set Manipulations3.1.2.1. RETRIEVAL OF ORTHOLOGOUS GENE SETSCurrently WebGestalt works only with human and mouse orthologs. To getthe orthologs: