title: A review of connectivity map and computational approaches in pharmacogenomics.
abstract: Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
authors.affiliation: Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.
authors.forename: Aliyu
authors.initials: A
authors.lastname: Musa
authors.affiliation: Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.
authors.forename: Laleh Soltan
authors.initials: LS
authors.lastname: Ghoraie
authors.affiliation: Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry BT47 6SB, Northern Ireland, UK.
authors.forename: Shu-Dong
authors.initials: SD
authors.lastname: Zhang
authors.affiliation: University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York 14642, USA.
authors.forename: Galina
authors.initials: G
authors.lastname: Glazko
authors.affiliation: Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.
authors.forename: Olli
authors.initials: O
authors.lastname: Yli-Harja
authors.affiliation: Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, 6060 Hall in Tyrol, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Dehmer
authors.affiliation: Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.|Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.|Department of Computer Science, University of Toronto, Toronto, ON, Canada.|Ontario Institute of Cancer Research, Toronto, ON, Canada.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
authors.affiliation: Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.
authors.forename: Frank
authors.initials: F
authors.lastname: Emmert-Streib
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D010597:Pharmacogenetics; D054852:Small Molecule Libraries / Q000494:pharmacology*; D059467:Transcriptome
chemical_list: D054852:Small Molecule Libraries