title: Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes.
abstract: One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, the quality of the keyword lists significantly affects the clustering results. We compared two keyword weighting schemes: normalised z-score and term frequency-inverse document frequency (TFIDF). Two gene sets were tested to evaluate the effectiveness of the weighting schemes for keyword extraction for gene clustering. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords outperformed those produced from normalised z-score weighted keywords. The optimised algorithms should be useful for partitioning genes from microarray lists into functionally discrete clusters.
authors.affiliation: Laboratory for Bioinformatics and Medical Informatics, Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083-0688, USA. ying.liu@utdallas.edu
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Shamkant B
authors.initials: SB
authors.lastname: Navathe
authors.forename: Alex
authors.initials: A
authors.lastname: Pivoshenko
authors.forename: Venu G
authors.initials: VG
authors.lastname: Dasigi
authors.forename: Ray
authors.initials: R
authors.lastname: Dingledine
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Ciliax
mesh_terms: D001330:Electronic Data Processing; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D005800:Genes, Fungal / Q000502:physiology*; D016239:MEDLINE; D012441:Saccharomyces cerevisiae / Q000502:physiology*; D018875:Vocabulary, Controlled