pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion.

Journal: Bioinformatics (Oxford, England)
Published Date: Jul 1, 2018

Abstract

MOTIVATION: Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model. We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations.

Authors

  • Ajay Anand Kumar
    Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
  • Lut Van Laer
    Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
  • Maaike Alaerts
    Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
  • Amin Ardeshirdavani
    Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Belgium.
  • Yves Moreau
    ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.
  • Kris Laukens
    Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium.
  • Bart Loeys
    Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
  • Geert Vandeweyer
    Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.

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