This repository contains the software Y2H-SCORES and supporting code for the publication Velásquez-Zapata et.al. (2021) Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor.
Y2H-SCORES is a software developed to rank protein-protein interactions from yeast two-hybrid next generation interaction screening (Y2H-NGIS) data. As a graphical summary of how the software works we present the Y2H-NGIS workflow and Y2H-SCORES. A) Experimental workflow for batch Y2H-NGIS. After the mating between bait and prey yeast cells, diploids go through a non-selective culture to reach exponential phase. Once there, the culture is split into two flasks, one for non-selection and another for selection. After reaching saturation in each condition, culture aliquots are taken to be sequenced. Schematic representation of the Y2H-SCORES, which consists of three ranking scores: B) enrichment score, which detects changes in prey proportions in selected and non-selected conditions. C) The specificity score measures differences in the prey enrichments with different baits under selection. D) The in-frame score identifies the enrichment of prey reading frames under selection, assigning higher values to in-frame preys.
Overview
The structure of this repository consists of two directories. In the Software directory all the functions and instructions to operate Y2H-SCORES can be found. The Publication directory contains all the supporting code for the publication, including the Y2H-NGIS simulator and the Benchmarking of the method with several datasets.
Y2H-SCORES has been published in PLoS Computational Biology, it can be accessed from https://doi.org/10.1371/journal.pcbi.1008890. Please refer to the paper for more details about each module. The entire pipeline has been coded in R.
Citations
If you use Y2H-SCORES, please cite
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Valeria Velásquez-Zapata, J Mitch Elmore, Sagnik Banerjee, Karin S Dorman, Roger P Wise (2021) Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PLoS Comput Biol 17(4): e1008890. https://doi.org/10.1371/journal.pcbi.1008890
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Sagnik Banerjee, Valeria Velásquez-Zapata, Gregory Fuerst, J Mitch Elmore, Roger P Wise (2020) NGPINT: a next-generation protein–protein interaction software. Briefings in Bioinformatics: bbaa351, https://doi.org/10.1093/bib/bbaa351