YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast

Tzu-Hsien Yang; Chia-Wei Hsu; Yan-Xiang Wang; Chien-Hung Yu; Jagat Rathod; Yan-Yuan Tseng; Wei-Sheng Wu

doi:10.1016/j.compbiomed.2022.106314

YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast

Comput Biol Med. 2022 Dec;151(Pt B):106314. doi: 10.1016/j.compbiomed.2022.106314. Epub 2022 Nov 14.

Authors

Tzu-Hsien Yang¹, Chia-Wei Hsu², Yan-Xiang Wang³, Chien-Hung Yu⁴, Jagat Rathod⁵, Yan-Yuan Tseng⁶, Wei-Sheng Wu⁷

Affiliations

¹ Department of Biomedical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan. Electronic address: thyangza@gs.ncku.edu.tw.
² Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan. Electronic address: q36081151@gs.ncku.edu.tw.
³ Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan. Electronic address: n26101143@gs.ncku.edu.tw.
⁴ Department of Biochemistry and Molecular Biology, National Cheng Kung University, University Road, 701 Tainan, Taiwan. Electronic address: Chien-hung.Yu@UTSouthwestern.edu.
⁵ Department of Environmental Biotechnology, Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar 382355, Gujarat, India. Electronic address: jagat.rathod@gbu.edu.in.
⁶ Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA. Electronic address: ytseng@wayne.edu.
⁷ Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan. Electronic address: wessonwu@mail.ncku.edu.tw.

PMID: 36455295
DOI: 10.1016/j.compbiomed.2022.106314

Abstract

Comparative analysis among multiple gene lists on their functional features is now a routine task due to the advancement of high-throughput experiments. Several enrichment analysis tools were developed in the past. However, these tools mainly focus on one gene list and contain only gene ontology or interaction features. What makes it worse, comparative investigation and customized feature set reanalysis are still unavailable. Therefore, we constructed the YMLA (Yeast Multiple List Analyzer) platform in this research. YMLA includes 39 yeast features and facilitates comparative analysis among multiple gene lists via tabular views, heatmaps, and network plots. Moreover, the customized feature set reanalysis function was implemented in YMLA to help form mechanism hypotheses based on a selected enriched feature subset. We demonstrated the biological applicability of YMLA via example lists consisting of genes with top/bottom translation efficiency values. The analysis results provided by YMLA reveal novel facts consistent with previous experiments. YMLA is available at https://cosbi7.ee.ncku.edu.tw/YMLA/.

Keywords: Functional enrichment; Functional mechanism deduction; Multiple gene list analysis.

Publication types

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

MeSH terms

Saccharomyces cerevisiae* / genetics
Software*