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
Pages
1-214
Date Issued
2021-12-01
Author(s)
Tsai, Ni Chiao
Hsu, Tzu Shu
Kuo, Shang Che
Kao, Chung Ting
Hung, Tzu Huan
Lin, Da Gin
Yeh, Chung Shu
Chu, Chia Chen
Lin, Jeng Shane
Lin, Hsin Hung
Chang, Tien Hsien
Su, Jung Chen
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
C++ | Deep-sea fishery | Precision agriculture | Preclinical drug discovery | Yeast one-hybrid
Other Subjects
data analysis; gene regulatory network; genetics; robotics; Saccharomyces cerevisiae; software; Data Analysis; Gene Regulatory Networks; Robotics; Saccharomyces cerevisiae; Software
Publisher
BioMed Central Ltd
Type
journal article