Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

Adel Dayarian; Gyan Bhanot; Feng Luo; Roberto Romero; Zhiming Wang; Michael Biehl; Erhan Bilal; Sahand Hormoz; Pablo Meyer; Raquel Norel; Kahn Rhrissorrakrai; Adi L Tarca

doi:10.1093/bioinformatics/btu490

Back

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

Journal article

Open access

Peer reviewed

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

Adel Dayarian, Gyan Bhanot, Feng Luo, Roberto Romero, Zhiming Wang, Michael Biehl, Erhan Bilal, Sahand Hormoz, Pablo Meyer, Raquel Norel, …

Bioinformatics (Oxford, England), Vol.31(4), pp.462-470

02/15/2015

DOI: https://doi.org/10.1093/bioinformatics/btu490

PMCID: PMC4325537

PMID: 25061067

Abstract

Animals

Cells, Cultured

Databases, Factual

Epithelial Cells - cytology

Epithelial Cells - metabolism

Gene Expression Profiling

Gene Expression Regulation

Gene Regulatory Networks

Humans

Lung - cytology

Lung - metabolism

Oligonucleotide Array Sequence Analysis

Phosphoproteins - metabolism

Rats

Species Specificity

Systems Biology - methods

Translational Medical Research

Algorithms

Phosphorylation

Software

Using gene expression to infer changes in protein phosphorylation levels induced in cells by various stimuli is an outstanding problem. The intra-species protein phosphorylation challenge organized by the IMPROVER consortium provided the framework to identify the best approaches to address this issue. Rat lung epithelial cells were treated with 52 stimuli, and gene expression and phosphorylation levels were measured. Competing teams used gene expression data from 26 stimuli to develop protein phosphorylation prediction models and were ranked based on prediction performance for the remaining 26 stimuli. Three teams were tied in first place in this challenge achieving a balanced accuracy of about 70%, indicating that gene expression is only moderately predictive of protein phosphorylation. In spite of the similar performance, the approaches used by these three teams, described in detail in this article, were different, with the average number of predictor genes per phosphoprotein used by the teams ranging from 3 to 124. However, a significant overlap of gene signatures between teams was observed for the majority of the proteins considered, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the union of the predictor genes of the three teams for multiple proteins. Gene expression and protein phosphorylation data are available from ArrayExpress (E-MTAB-2091). Software implementation of the approach of Teams 49 and 75 are available at http://bioinformaticsprb.med.wayne.edu and http://people.cs.clemson.edu/∼luofeng/sbv.rar, respectively. gyanbhanot@gmail.com or luofeng@clemson.edu or atarca@med.wayne.edu Supplementary data are available at Bioinformatics online.

Files and links (1)

url

https://doi.org/10.1093/bioinformatics/btu490View

Version of Record (VoR) Open

Metrics

7 Record Views

8 Times Cited - Web of Science

See more details

Details

Title: Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge
Creators: Adel Dayarian - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Gyan Bhanot - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Feng Luo - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Roberto Romero - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Zhiming Wang - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Michael Biehl - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Erhan Bilal - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Sahand Hormoz - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Pablo Meyer - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Raquel Norel - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Kahn Rhrissorrakrai - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Adi L Tarca - Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
Publication Details: Bioinformatics (Oxford, England), Vol.31(4), pp.462-470
Date published: 02/15/2015
Grant note: HHSN275201300006C / NICHD NIH HHS HHSN275201300006C / PHS HHS
Academic Unit: Molecular Biology and Biochemistry (SAS)
Language: English
Resource Type: Journal article
Identifiers: 991031666080804646