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

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.

Results

We present two approaches, ranked second in this challenge, that do not rely o

SUBMITTER: Hafemeister C 

PROVIDER: S-EPMC4325539 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature