Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Ni-Chiao Tsai; Tzu-Shu Hsu; Shang-Che Kuo; Chung-Ting Kao; Tzu-Huan, Hung; Da-Gin Lin; Chung-Shu Yeh; Chia-Chen Chu; Jeng-Shane Lin; Hsin-Hung Lin; Chia-Ying Ko; Tien-Hsien Chang; Jung-Chen Su; Ying-Chung Jimmy Lin

doi:10.1186/s12915-021-01140-y

Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Journal

BMC Biology

Journal Volume

19

Journal Issue

1

Start Page

214

Date Issued

2021-09

Author(s)

Ni-Chiao Tsai

Tzu-Shu Hsu

Shang-Che Kuo

Chung-Ting Kao

Tzu-Huan, Hung

農業部農業試驗所

Da-Gin Lin

Chung-Shu Yeh

Chia-Chen Chu

Jeng-Shane Lin

Hsin-Hung Lin

Chia-Ying Ko

Tien-Hsien Chang

Jung-Chen Su

Ying-Chung Jimmy Lin

DOI

10.1186/s12915-021-01140-y

URI

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01140-y

https://scholars.tari.gov.tw/handle/123456789/16287

Abstract

Background Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. Results We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. Conclusions The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.

Subjects

Yeast one-hybrid

C plus plus

Preclinical drug discovery

Precision agriculture

Deep-sea fishery

Publisher

BMC Campus

Type

journal article