Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Journal: Bioinformatics (Oxford, England)
Published Date: Aug 22, 2014

Abstract

MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER Species Translation Challenge, where 52 stimuli were applied to both human and rat cells and perturbed pathways were identified. In the Inter-species Pathway Perturbation Prediction sub-challenge, multiple teams proposed methods to use rat transcription data from 26 stimuli to predict human gene set and pathway activity under the same perturbations. Submissions were evaluated using three performance metrics on data from the remaining 26 stimuli.

Authors

  • Christoph Hafemeister
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Roberto Romero
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Erhan Bilal
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Pablo Meyer
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Raquel Norel
    IBM Research, Yorktown Heights, NY, USA. rnorel@us.ibm.com.
  • Kahn Rhrissorrakrai
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Richard Bonneau
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.
  • Adi L Tarca
    Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD and Detroit, MI 48201, USA, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, Computer Science Department, Courant institute of Mathematical Sciences, New York University, New York, NY 10012 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.

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