Correspondence Author. Abstract.pdf

Comparison of Two Schemes for Automatic Keyword Extraction from MEDLINE for Functional Gene Clustering Ying Liu College of Computing Georgia Institute of Technology Atlanta, Ga 30332-0280 yingliu@ Brian J. Ciliax Department of Neurology Emory University Sch Medicine Atlanta, Ga 30322 bciliax@ Karin Borges Department of Pharmacology Emory University Sch Med Atlanta, Ga 30322 kborges@ Venu Dasigi Southern Polytechnic State University Marietta, Ga 30060 vdasigi@ Ashwin Ram College of Computing Georgia Institute of Technology Atlanta, Ga 30332-0280 ashwin@ Shamkant B. Navathe College of Computing Georgia Institute of Technology Atlanta, Ga 30332-0280 sham@ Ray Dingledine* Department of Pharmacology Emory University Sch Med Atlanta, Ga 30322 rdingledine@ * Correspondence Author. Abstract One of the key challenges of microarray studies is to derive biological insights from the unprecedented quantities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describe the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency– inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF