SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.

Abstract

UNLABELLED Significance Analysis of INTeractome (SAINT) is a statistical method for probabilistically scoring protein-protein interaction data from affinity purification-mass spectrometry (AP-MS) experiments. The utility of the software has been demonstrated in many protein-protein interaction mapping studies, yet the extensive testing also revealed some practical drawbacks. In this paper, we present a new implementation, SAINTexpress, with simpler statistical model and quicker scoring algorithm, leading to significant improvements in computational speed and sensitivity of scoring. SAINTexpress also incorporates external interaction data to compute supplemental topology-based scores to improve the likelihood of identifying co-purifying protein complexes in a probabilistically objective manner. Overall, these changes are expected to improve the performance and user experience of SAINT across various types of high quality datasets. BIOLOGICAL SIGNIFICANCE We present SAINTexpress, an upgraded implementation of Significance Analysis of INTeractome (SAINT) for filtering high confidence interaction data from affinity purification-mass spectrometry (AP-MS) experiments. SAINTexpress features faster computation and incorporation of external data sources into the scoring, improving the performance and user experience of SAINT across various types of datasets. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?

DOI: 10.1016/j.jprot.2013.10.023
05020132014201520162017
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@article{Teo2014SAINTexpressIA, title={SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.}, author={Guoci Teo and Guomin Liu and Jianping Zhang and Alexey I. Nesvizhskii and Anne-Claude Gingras and Hyungwon Choi}, journal={Journal of proteomics}, year={2014}, volume={100}, pages={37-43} }