title: Cross-organism learning method to discover new gene functionalities.
abstract: BACKGROUND
  Knowledge of gene and protein functions is paramount for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. Analyses for biomedical knowledge discovery greatly benefit from the availability of gene and protein functional feature descriptions expressed through controlled terminologies and ontologies, i.e., of gene and protein biomedical controlled annotations. In the last years, several databases of such annotations have become available; yet, these valuable annotations are incomplete, include errors and only some of them represent highly reliable human curated information. Computational techniques able to reliably predict new gene or protein annotations with an associated likelihood value are thus paramount.
  
  
  METHODS
  Here, we propose a novel cross-organisms learning approach to reliably predict new functionalities for the genes of an organism based on the known controlled annotations of the genes of another, evolutionarily related and better studied, organism. We leverage a new representation of the annotation discovery problem and a random perturbation of the available controlled annotations to allow the application of supervised algorithms to predict with good accuracy unknown gene annotations. Taking advantage of the numerous gene annotations available for a well-studied organism, our cross-organisms learning method creates and trains better prediction models, which can then be applied to predict new gene annotations of a target organism.
  
  
  RESULTS
  We tested and compared our method with the equivalent single organism approach on different gene annotation datasets of five evolutionarily related organisms (Homo sapiens, Mus musculus, Bos taurus, Gallus gallus and Dictyostelium discoideum). Results show both the usefulness of the perturbation method of available annotations for better prediction model training and a great improvement of the cross-organism models with respect to the single-organism ones, without influence of the evolutionary distance between the considered organisms. The generated ranked lists of reliably predicted annotations, which describe novel gene functionalities and have an associated likelihood value, are very valuable both to complement available annotations, for better coverage in biomedical knowledge discovery analyses, and to quicken the annotation curation process, by focusing it on the prioritized novel annotations predicted.
authors.affiliation: DISI, Università degli Studi di Bologna, Via Venezia 52, 47521 Cesena, Italy. Electronic address: giacomo.domeniconi@unibo.it.
authors.forename: Giacomo
authors.initials: G
authors.lastname: Domeniconi
authors.affiliation: DEIB, Politecnico di Milano, Piazza L. Da Vinci 32, 20133 Milan, Italy. Electronic address: masseroli@elet.polimi.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Masseroli
authors.affiliation: DISI, Università degli Studi di Bologna, Via Venezia 52, 47521 Cesena, Italy. Electronic address: gianluca.moro@unibo.it.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Moro
authors.affiliation: DEIB, Politecnico di Milano, Piazza L. Da Vinci 32, 20133 Milan, Italy. Electronic address: pinoli@elet.polimi.it.
authors.forename: Pietro
authors.initials: P
authors.lastname: Pinoli
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D004023:Dictyostelium; D023281:Genomics; D006801:Humans; D016013:Likelihood Functions; D051379:Mice; D015233:Models, Statistical; D058977:Molecular Sequence Annotation / Q000379:methods*; D010641:Phenotype; D010802:Phylogeny; D040901:Proteomics; D015203:Reproducibility of Results; D012660:Semantics; D012984:Software; D013045:Species Specificity; D018875:Vocabulary, Controlled
keywords: Biomolecular annotation prediction; Data representation; Discrete matrix completion; Gene ontology; Knowledge discovery; Transfer learning