Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of different
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RESEARCH
Open Access
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes Peng-Cheng Chen1†, Li Ruan2†, Jie Jin2, Yu-Tian Tao2, Xiao-Bao Ding2, Hai-bo Zhang2, Wen-Ping Guo2, Qiao-lei Yang1, Heng Yao1 and Xin Chen1,2,3*
Abstract Background: The 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. Results: We 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. Conclusion: We 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. Keywords: Caenorhabditis elegans, Functional interaction, Database, Gene set linkage analysis, Transcriptomic analysis tool
* Correspondence: [email protected] † Peng-Cheng Chen and Li Ruan contributed equally to this work. 1 Institute of Pharmaceutical Biotechnology of Zhejiang University School of Medicine and Department of Radiology of the First Affiliated Hospital, Hangzhou 310058, China 2 Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou 318000, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Com
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