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Getting Started: Loading Gene and Experiment Sets

Tab-delimited file: These files have a .tab extension. The first row is a header row, where the names of the sets are specified from column 2 and on. The second row and on specify the gene or experiment (depending on whether this is a gene or experiment sets file) membership in the sets, where the first column is the unique identifier of each gene or experiment, and column 2 and on specify the gene membership, where '0' indicates that the gene or experiment do not belong to the set for that column, '1' indicates that it does belong, and an empty blank column indicates that the membership is not known. The sample directory contains two sample .tab sets files, one for genes and one for experiments.

Genomica formatted file: These files have a proprietary format with the extension '.gxa' and can represent sets that are more complex than binary assignments (e.g., continuous values or sets with various category values). You can convert a .tab delimited set file into a .gxa formatted file by loading the .tab file and then saving it as a .gxa file from the Sets -> View Sets menu followed by selecting the Save to File option. The sample directory contains two sample .gxa sets files, one for genes and one for experiments.

You can load a gene set file from the Sets -> Load Gene Sets From File... or Sets -> Load Gene Sets From Repository... menu (select the .tab extension for loading tab files), and similarly for experiment sets. After loading sets, you can view all the currenty available gene sets (and similar for experiment sets) using the Sets -> View Gene Sets menu. From that menu, you can then Edit sets to remove member sets from them, create new collections of gene sets (using the Add option), delete entire gene set collections from Genomica (using the Remove option), and also obtain a graphical representation of gene set collections (using the View option). For the gene and experiment sets in the sample file, the View option should result in a view similar to the following: