title: An unsupervised approach to predict functional relations between genes based on expression data.
abstract: This work presents a novel approach to predict functional relations between genes using gene expression data. Genes may have various types of relations between them, for example, regulatory relations, or they may be concerned with the same protein complex or metabolic/signaling pathways and obviously gene expression data should contain some clues to such relations. The present approach first digitizes the log-ratio type gene expression data of S. cerevisiae to a matrix consisting of 1, 0, and -1 indicating highly expressed, no major change, and highly suppressed conditions for genes, respectively. For each gene pair, a probability density mass function table is constructed indicating nine joint probabilities. Then gene pairs were selected based on linear and probabilistic relation between their profiles indicated by the sum of probability density masses in selected points. The selected gene pairs share many Gene Ontology terms. Furthermore a network is constructed by selecting a large number of gene pairs based on FDR analysis and the clustering of the network generates many modules rich with similar function genes. Also, the promoters of the gene sets in many modules are rich with binding sites of known transcription factors indicating the effectiveness of the proposed approach in predicting regulatory relations.
authors.affiliation: Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.affiliation: Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors.forename: Tetsuo
authors.identifier: 0000-0003-1327-0854
authors.initials: T
authors.lastname: Katsuragi
authors.affiliation: Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Sato
authors.affiliation: Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.affiliation: Computational Systems Biology Lab, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D001185:Artificial Intelligence; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D005810:Multigene Family / Q000502:physiology; D010363:Pattern Recognition, Automated / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors