|
1
|
Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S. Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. Bioinformatics 2014; 31:453-61. [PMID: 24994890 PMCID: PMC4325536 DOI: 10.1093/bioinformatics/btu407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Animal models are widely used in biomedical research for reasons ranging from practical to ethical. An important issue is whether rodent models are predictive of human biology. This has been addressed recently in the framework of a series of challenges designed by the systems biology verification for Industrial Methodology for Process Verification in Research (sbv IMPROVER) initiative. In particular, one of the sub-challenges was devoted to the prediction of protein phosphorylation responses in human bronchial epithelial cells, exposed to a number of different chemical stimuli, given the responses in rat bronchial epithelial cells. Participating teams were asked to make inter-species predictions on the basis of available training examples, comprising transcriptomics and phosphoproteomics data. RESULTS Here, the two best performing teams present their data-driven approaches and computational methods. In addition, post hoc analyses of the datasets and challenge results were performed by the participants and challenge organizers. The challenge outcome indicates that successful prediction of protein phosphorylation status in human based on rat phosphorylation levels is feasible. However, within the limitations of the computational tools used, the inclusion of gene expression data does not improve the prediction quality. The post hoc analysis of time-specific measurements sheds light on the signaling pathways in both species. AVAILABILITY AND IMPLEMENTATION A detailed description of the dataset, challenge design and outcome is available at www.sbvimprover.com. The code used by team IGB is provided under http://github.com/uci-igb/improver2013. Implementations of the algorithms applied by team AMG are available at http://bhanot.biomaps.rutgers.edu/wiki/AMG-sc2-code.zip. CONTACT meikelbiehl@gmail.com.
Collapse
Affiliation(s)
- Michael Biehl
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Peter Sadowski
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Gyan Bhanot
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Erhan Bilal
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Adel Dayarian
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Pablo Meyer
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Raquel Norel
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Kahn Rhrissorrakrai
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Michael D Zeller
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Sahand Hormoz
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| |
Collapse
|