Jun 15, 2015

Overcoming analytical reliability issues in clinical proteomics using rank-based network approaches

BioRxiv : the Preprint Server for Biology
Wilson Wen Bin Goh, Limsoon Wong

Abstract

Proteomics is poised to play critical roles in clinical research. However, due to limited coverage and high noise, integration with powerful analysis algorithms is necessary. In particular, network-based algorithms can improve selection of reproducible features in spite of incomplete proteome coverage, technical inconsistency or high inter-sample variability. We define analytical reliability on three benchmarks \---| precision/recall rates, feature-selection stability and cross-validation accuracy. Using these, we demonstrate the insufficiencies of commonly used Student???s t-test and Hypergeometric enrichment. Given advances in sample sizes, quantitation accuracy and coverage, we are now able to introduce and evaluate Ranked-Based Network Approaches (RBNAs) for the first time in proteomics. These include SNET (SubNETwork), FSNET (FuzzySNET), PFSNET (PairedFSNET). We also introduce for the first time, PPFSNET(samplePairedPFSNET), which is a paired-sample variant of PFSNET. RBNAs (particularly PFSNET and PPFSNET) excelled on all three benchmarks and can make consistent and reproducible predictions even in the small-sample size scenario (n=4). Given these qualities, RBNAs represent an important advancement in network biology, and...Continue Reading

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Mentioned in this Paper

Biological Markers
Laboratory Procedures
Cross Validation
Evaluation
Proteomics
Proteome
Student
Analysis
Clinical Research
Enzyme Stability

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