Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles

PLoS Computational Biology
Minseung KimIlias Tagkopoulos

Abstract

A tantalizing question in cellular physiology is whether the cellular state and environmental conditions can be inferred by the expression signature of an organism. To investigate this relationship, we created an extensive normalized gene expression compendium for the bacterium Escherichia coli that was further enriched with meta-information through an iterative learning procedure. We then constructed an ensemble method to predict environmental and cellular state, including strain, growth phase, medium, oxygen level, antibiotic and carbon source presence. Results show that gene expression is an excellent predictor of environmental structure, with multi-class ensemble models achieving balanced accuracy between 70.0% (±3.5%) to 98.3% (±2.3%) for the various characteristics. Interestingly, this performance can be significantly boosted when environmental and strain characteristics are simultaneously considered, as a composite classifier that captures the inter-dependencies of three characteristics (medium, phase and strain) achieved 10.6% (±1.0%) higher performance than any individual models. Contrary to expectations, only 59% of the top informative genes were also identified as differentially expressed under the respective conditi...Continue Reading

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Citations

Apr 29, 2015·ACS Synthetic Biology·Linh Huynh, Ilias Tagkopoulos
Dec 29, 2016·Neural Computation·Saket Navlakha
Dec 12, 2018·Biotechnology and Bioengineering·Navneet RaiIlias Tagkopoulos
Oct 12, 2017·Nature Biotechnology·Jonathan M MonkBernhard O Palsson
Nov 19, 2015·Molecular Systems Biology·Mario L Arrieta-OrtizPatrick Eichenberger
May 5, 2018·Molecular Omics·Minseung Kim, Ilias Tagkopoulos
Sep 5, 2018·Nature Communications·Xiaokang WangIlias Tagkopoulos
Feb 3, 2021·PLoS Computational Biology·Anand V SastryBernhard O Palsson

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Methods Mentioned

BETA
RNA-Seq
gene knock-outs

Software Mentioned

PortEco
M3D
EcoCyc
RSEQ
MATLAB
DAVID
ArrayExpress
NaiveBayes
bgrQuantifier
ClassificationTree

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