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; Rathod Jagat; 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

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

Research output: Contribution to journal › Article › peer-review

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/.

Original language	English
Article number	106314
Journal	Computers in Biology and Medicine
Volume	151
DOIs	https://doi.org/10.1016/j.compbiomed.2022.106314
Publication status	Published - 2022 Dec

All Science Journal Classification (ASJC) codes

Computer Science Applications
Health Informatics

Access to Document

10.1016/j.compbiomed.2022.106314

Cite this

@article{16d0fb562937400c8f74c329f55e306f,

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

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/.",

author = "Yang, {Tzu Hsien} and Hsu, {Chia Wei} and Wang, {Yan Xiang} and Yu, {Chien Hung} and Rathod Jagat and Tseng, {Yan Yuan} and Wu, {Wei Sheng}",

note = "Funding Information: This work was supported by National Cheng Kung University and the National Science and Technology Council of Taiwan [ MOST 108-2628-E-006-004-MY3 , MOST 111-2636-B-006-013 , MOST 110-2221-E-006-198-MY3 , MOST 111-2221-E-006-151-MY3 , MOST 110-2222-E-006-017 , and MOST 111-2221-E-006-231 ]. Publisher Copyright: {\textcopyright} 2022 Elsevier Ltd",

year = "2022",

month = dec,

doi = "10.1016/j.compbiomed.2022.106314",

language = "English",

volume = "151",

journal = "Computers in Biology and Medicine",

issn = "0010-4825",

publisher = "Elsevier Limited",

}

TY - JOUR

T1 - YMLA

T2 - A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast

AU - Yang, Tzu Hsien

AU - Hsu, Chia Wei

AU - Wang, Yan Xiang

AU - Yu, Chien Hung

AU - Jagat, Rathod

AU - Tseng, Yan Yuan

AU - Wu, Wei Sheng

N1 - Funding Information: This work was supported by National Cheng Kung University and the National Science and Technology Council of Taiwan [ MOST 108-2628-E-006-004-MY3 , MOST 111-2636-B-006-013 , MOST 110-2221-E-006-198-MY3 , MOST 111-2221-E-006-151-MY3 , MOST 110-2222-E-006-017 , and MOST 111-2221-E-006-231 ]. Publisher Copyright: © 2022 Elsevier Ltd

PY - 2022/12

Y1 - 2022/12

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=85142900383&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85142900383&partnerID=8YFLogxK

U2 - 10.1016/j.compbiomed.2022.106314

DO - 10.1016/j.compbiomed.2022.106314

M3 - Article

C2 - 36455295

AN - SCOPUS:85142900383

SN - 0010-4825

VL - 151

JO - Computers in Biology and Medicine

JF - Computers in Biology and Medicine

M1 - 106314

ER -

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

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this