NTP-led team creates sentinel gene set for exposures studies
Researchers from the National Toxicology Program (NTP) and NIEHS partnered with members of the Tox21 project and the bioinformatics company SciOme to determine a set of genes to use to detect human responses to exposures or diseases. The authors created the S1500-plus list by applying mathematical analyses of publicly available data on nearly 78,000 samples to identify highly informative sentinel genes.
The genes in the group were first selected by their power to differentiate between control and exposed samples. They were ranked for their capacity to predict the levels of other genes. The scientists then optimized the selection for maximal representation of all major biological functions. Finally, the scientific community nominated additional genes. After the data- and knowledge-driven effort, 2,739 genes were included in the S1500-plus gene set. Although this is only 15 percent of the total number of human genes, the set accurately detects human responses to chemicals and disease processes.
The gene set allowed the authors to predict levels of unmeasured genes and biological functions with high confidence. The scientists explained that detection of the S1500-plus genes might be sufficient to understand the overall response. The lower cost of measuring only the S1500-plus genes will speed up studies using with large numbers of people or samples. (DGS)
Citation: Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, Judson RS, Karmaus AL, Maull EA, Mendrick DL, Merrick BA, Sipes NS, Svoboda D, Paules RS. 2018. A hybrid gene selection approach to create the S1500-plus targeted gene sets for use in high-throughput transcriptomics. PLoS One 13(2):e0191105.