Title: PgenePapers: a novel database and search tools of reported regulatory pseudogenes

Authors: Achal Awasthi; Shenglong Tan; Travis S. Johnson; Xiaokui-Molly Mo; Kunjie Fan; Yan Zhang

Addresses: Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA ' Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA; School of Information Engineering, Hubei University of Economics, Wuhan, Hubei, 430205, China ' Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA; Department of Medicine, Indiana University School of Medicine, 545 Barnhill Drive, Indianapolis, IN, 46202, USA ' Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA ' Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA ' Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center (OSUCCC – James), Columbus, OH, 43210, USA

Abstract: Background: Pseudogenes are non-coding relatives of genes. Recent studies have shown that a considerable number of pseudogenes are transcribed, and some of them can regulate gene expression. Studies have detected pseudogene differential expression in cancer subtypes, indicating potential impact of pseudogenes on cancer development and clinical outcomes. Pseudogenes make a new class of expression modulators. However, there is not yet a database focusing on regulatory roles of pseudogenes. Methods: We constructed the regulatory networks involving pseudogenes and genes with disease and tissue specific annotations, and further included potential miRNAs and drugs targeting components of the networks, based on expression profiles, miRNA binding predictions and FDA approved drugs. Results and conclusion: We developed the first comprehensive database of reported regulatory pseudogenes, and developed the PgenePapers app which allows flexible database search and provides network visualisation. PgenePapers provides a knowledgebase upon which we can develop methods for pseudogene function prediction and validation.

Keywords: regulatory pseudogene; database; search tools; graph presentation; correlation network; Shiny app.

DOI: 10.1504/IJCBDD.2020.113820

International Journal of Computational Biology and Drug Design, 2020 Vol.13 No.5/6, pp.504 - 519

Received: 04 Oct 2019
Accepted: 22 Apr 2020
Published online: 31 Mar 2021 *

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