Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data

Valeria Velásquez-Zapata; J Mitch Elmore; Roger P Wise

doi:10.1007/978-1-0716-3327-4_20

Bioinformatic Analysis of Yeast Two-Hybrid Next-Generation Interaction Screen Data

Methods Mol Biol. 2023:2690:223-239. doi: 10.1007/978-1-0716-3327-4_20.

Authors

Valeria Velásquez-Zapata^{1

2}, J Mitch Elmore^{3

4

5}, Roger P Wise^{6

7

8}

Affiliations

¹ Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA. vvelasqz@iastate.edu.
² Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA. vvelasqz@iastate.edu.
³ Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA.
⁴ USDA-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, USA.
⁵ USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA.
⁶ Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, USA. roger.wise@usda.gov.
⁷ Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, USA. roger.wise@usda.gov.
⁸ USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research, Ames, IA, USA. roger.wise@usda.gov.

PMID: 37450151
DOI: 10.1007/978-1-0716-3327-4_20

Abstract

Yeast two-hybrid next-generation interaction screening (Y2H-NGIS) uses the output of next-generation sequencing to mine for novel protein-protein interactions. Here, we outline the analytics underlying Y2H-NGIS datasets. Different systems, libraries, and experimental designs comprise Y2H-NGIS methodologies. We summarize the analysis in several layers that comprise the characterization of baits and preys, quantification, and identification of true interactions for subsequent secondary validation. We present two software designed for this purpose, NGPINT and Y2H-SCORES, which are used as front-end and back-end tools in the analysis. Y2H-SCORES software can be used and adapted to analyze different datasets not only from Y2H-NGIS but from other techniques ruled by similar biological principles.

Keywords: Next Generation Interaction Screening (NGIS); Systems biology; Yeast two-hybrid (Y2H); interaction prediction; ranking interactions.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology*
Saccharomyces cerevisiae* / genetics
Two-Hybrid System Techniques