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

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 netw...

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Bibliographic Details
Published in:Biology direct 2020-10, Vol.15 (1), p.20-20, Article 20
Main Authors: Chen, Peng-Cheng, Ruan, Li, Jin, Jie, Tao, Yu-Tian, Ding, Xiao-Bao, Zhang, Hai-Bo, Guo, Wen-Ping, Yang, Qiao-Lei, Yao, Heng, Chen, Xin
Format: Article
Language:English
Subjects:
Caenorhabditis elegans
Case studies
Developmental biology
Functional interaction
Gene set linkage analysis
Genes
Neurophysiology
Transcriptomic analysis tool
Web site management software
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Summary: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. 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. 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 .
ISSN:1745-6150
1745-6150
DOI:10.1186/s13062-020-00271-6