Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes

Biology Direct

Jie Jin¹  Hai-bo Zhang¹  Li Ruan¹  Wen-Ping Guo¹  Yu-Tian Tao¹  Xiao-Bao Ding¹  Peng-Cheng Chen²  Qiao-lei Yang²  Heng Yao²  Xin Chen³ 

[1] Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 318000, Taizhou, China;Institute of Pharmaceutical Biotechnology of Zhejiang University School of Medicine and Department of Radiology of the First Affiliated Hospital, 310058, Hangzhou, China;Institute of Pharmaceutical Biotechnology of Zhejiang University School of Medicine and Department of Radiology of the First Affiliated Hospital, 310058, Hangzhou, China;Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, 318000, Taizhou, China;Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, 310058, Hangzhou, China;

关键词: Caenorhabditis elegans;    Functional interaction;    Database;    Gene set linkage analysis;    Transcriptomic analysis tool;   

DOI  :  10.1186/s13062-020-00271-6

来源: Springer

【 摘 要 】

BackgroundThe nematode worm, Caenorhabditis elegans, is a saprophytic species that has been emerging as a standard model organism since the early 1960s. This species is useful in numerous fields, including developmental biology, neurobiology, and ageing. A high-quality comprehensive molecular interaction network is needed to facilitate molecular mechanism studies in C. elegans.ResultsWe present the predicted functional interactome of Caenorhabditis elegans (FIC), which integrates functional association data from 10 public databases to infer functional gene interactions on diverse functional perspectives. In this work, FIC includes 108,550 putative functional associations with balanced sensitivity and specificity, which are expected to cover 21.42% of all C. elegans protein interactions, and 29.25% of these associations may represent protein interactions. Based on FIC, we developed a gene set linkage analysis (GSLA) web tool to interpret potential functional impacts from a set of differentially expressed genes observed in transcriptome analyses.ConclusionWe present the predicted C. elegans interactome database FIC, which is a high-quality database of predicted functional interactions among genes. The functional interactions in FIC serve as a good reference interactome for GSLA to annotate differentially expressed genes for their potential functional impacts. In a case study, the FIC/GSLA system shows more comprehensive and concise annotations compared to other widely used gene set annotation tools, including PANTHER and DAVID. FIC and its associated GSLA are available at the website http://worm.biomedtzc.cn.

【 授权许可】

CC BY