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Significance Biological systems function through the interaction of numerous molecules influencing a variety of biochemical reactions. However, most biological systems are still only partially understood. This paper introduces GeneFishing, a method for “fishing out” candidate genes in a biological process. The method is “semisupervised” using a set of “bait” genes (i.e., ones previously known to be relevant to the same process). GeneFishing effectively combines modern and traditional statistical ideas for analyzing both big and small data. We applied this method to cholesterol-related genes and identified several interesting phenomena. GeneFishing has the potential for pointing to functional importance in known but poorly studied genes, and its underlying framework is broadly applicable inside and outside biology.

GeneFishing to reconstruct context specific portraits of biological processes