FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery

Jianing Gao; Huan Zhang; Xiaohua Jiang; Asim Ali; Daren Zhao; Jianqiang Bao; Long Jiang; Furhan Iqbal; Qinghua Shi; Yuanwei Zhang

doi:10.1016/j.gpb.2021.08.010

FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery

Genomics Proteomics Bioinformatics. 2022 Jun;20(3):455-465. doi: 10.1016/j.gpb.2021.08.010. Epub 2021 Dec 24.

Authors

Affiliations

¹ The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Hefei 230027, China.
² The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Hefei 230027, China. Electronic address: biojxh@mail.ustc.edu.cn.
³ The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Hefei 230027, China. Electronic address: qshi@ustc.edu.cn.
⁴ The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Hefei 230027, China. Electronic address: zyuanwei@ustc.edu.cn.

Abstract

Exploring the genetic basis of human infertility is currently under intensive investigation. However, only a handful of genes have been validated in animal models as disease-causing genes in infertile men. Thus, to better understand the genetic basis of human spermatogenesis and bridge the knowledge gap between humans and other animal species, we construct the FertilityOnline, a database integrating the literature-curated functional genes during spermatogenesis into an existing spermatogenic database, SpermatogenesisOnline 1.0. Additional features, including the functional annotation and genetic variants of human genes, are also incorporated into FertilityOnline. By searching this database, users can browse the functional genes involved in spermatogenesis and instantly narrow down the number of candidates of genetic mutations underlying male infertility in a user-friendly web interface. Clinical application of this database was exampled by the identification of novel causative mutations in synaptonemal complex central element protein 1 (SYCE1) and stromal antigen 3 (STAG3) in azoospermic men. In conclusion, FertilityOnline is not only an integrated resource for spermatogenic genes but also a useful tool facilitating the exploration of the genetic basis of male infertility. FertilityOnline can be freely accessed at http://mcg.ustc.edu.cn/bsc/spermgenes2.0/index.html.

Keywords: Database; FertilityOnline; Functional gene; Infertility; Mutation.

Publication types

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

MeSH terms

Cell Cycle Proteins / genetics
DNA Mutational Analysis* / methods
Databases, Genetic*
Humans
Infertility, Male* / genetics
Male
Molecular Sequence Annotation* / methods
Mutation
Online Systems
Spermatogenesis* / genetics

Substances

Cell Cycle Proteins
STAG3 protein, human