Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

Zhiyuan Zhang; Guozhong Chen; Jun Hu; Wajid Hussain; Fenxia Fan; Yalin Yang; Zhigang Zhou; Xiaodong Fang; Jun Zhu; Wei-Hua Chen; Zhi Liu

doi:10.1093/database/baz069

Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

Database (Oxford). 2019 Jan 1:2019:baz069. doi: 10.1093/database/baz069.

Authors

Zhiyuan Zhang¹, Guozhong Chen¹, Jun Hu¹, Wajid Hussain¹, Fenxia Fan², Yalin Yang³, Zhigang Zhou³, Xiaodong Fang⁴, Jun Zhu¹, Wei-Hua Chen^{1

5

6}, Zhi Liu¹

Affiliations

¹ Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
² State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
³ Sino-Norway Fish Gastrointestinal Microbiota Joint Lab, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
⁴ The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Bioinformatics Group, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
⁵ College of Life Science, Henan Normal University, Xinxiang 453007, China.
⁶ Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou, Hubei 436044, China.

Abstract

Gram-negative bacterium Vibrio cholerae is the causative agent of cholera, a life-threatening diarrheal disease. During its infectious cycle, V. cholerae routinely switches niches between aquatic environment and host gastrointestinal tract, in which V. cholerae modulates its transcriptome pattern accordingly for better survival and proliferation. A comprehensive resource for V. cholerae transcriptome will be helpful for cholera research, including prevention, diagnosis and intervention strategies. In this study, we constructed a microarray and RNA-seq database of V. cholerae (Mr.Vc), containing gene transcriptional expression data of 145 experimental conditions of V. cholerae from various sources, covering 25 937 entries of differentially expressed genes. In addition, we collected relevant information including gene annotation, operons they may belong to and possible interaction partners of their protein products. With Mr.Vc, users can easily find transcriptome data they are interested in, such as the experimental conditions in which a gene of interest was differentially expressed in, or all genes that were differentially expressed in an experimental condition. We believe that Mr.Vc database is a comprehensive data repository dedicated to V. cholerae and could be a useful resource for all researchers in related fields. Mr.Vc is available for free at http://bioinfo.life.hust.edu.cn/mrvc.

Publication types

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

MeSH terms

Bacterial Proteins* / biosynthesis
Bacterial Proteins* / genetics
Databases, Nucleic Acid*
Gene Expression Profiling
Gene Expression Regulation, Bacterial*
Humans
RNA, Bacterial* / biosynthesis
RNA, Bacterial* / genetics
RNA-Seq*
Transcriptome*
Vibrio cholerae* / genetics
Vibrio cholerae* / metabolism

Substances

Bacterial Proteins
RNA, Bacterial