HGD: an Integrated Homologous Gene Database Across Multiple Species

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2022 Nov 1

PMID 36318261

Authors

Guangya Duan

Gangao Wu

Xiaoning Chen

Dongmei Tian

Zhaohua Li

Yanling Sun

Zhenglin Du

Lili Hao

Shuhui Song

Yuan Gao

Jingfa Xiao

Zhang Zhang

Yiming Bao

Bixia Tang

Wenming Zhao

Affiliations

Soon will be listed here.

Abstract

Homology is fundamental to infer genes' evolutionary processes and relationships with shared ancestry. Existing homolog gene resources vary in terms of inferring methods, homologous relationship and identifiers, posing inevitable difficulties for choosing and mapping homology results from one to another. Here, we present HGD (Homologous Gene Database, https://ngdc.cncb.ac.cn/hgd), a comprehensive homologs resource integrating multi-species, multi-resources and multi-omics, as a complement to existing resources providing public and one-stop data service. Currently, HGD houses a total of 112 383 644 homologous pairs for 37 species, including 19 animals, 16 plants and 2 microorganisms. Meanwhile, HGD integrates various annotations from public resources, including 16 909 homologs with traits, 276 670 homologs with variants, 398 573 homologs with expression and 536 852 homologs with gene ontology (GO) annotations. HGD provides a wide range of omics gene function annotations to help users gain a deeper understanding of gene function.

Citing Articles

Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms.

Cho D, Lee H, Kim J, Song J, Hwang S, Lee B Database (Oxford). 2024; 2024.

PMID: 39192607 PMC: 11349611. DOI: 10.1093/database/baae085.

Cellular dynamics in pig-to-human kidney xenotransplantation.

Pan W, Zhang W, Zheng B, Camellato B, Stern J, Lin Z Med. 2024; 5(8):1016-1029.e4.

PMID: 38776915 PMC: 11317223. DOI: 10.1016/j.medj.2024.05.003.

BioKA: a curated and integrated biomarker knowledgebase for animals.

Wang Y, Lin Y, Wu S, Sun J, Meng Y, Jin E Nucleic Acids Res. 2023; 52(D1):D1121-D1130.

PMID: 37843156 PMC: 10767812. DOI: 10.1093/nar/gkad873.

TCOD: an integrated resource for tropical crops.

Kang H, Huang T, Duan G, Meng Y, Chen X, He S Nucleic Acids Res. 2023; 52(D1):D1651-D1660.

PMID: 37843152 PMC: 10767838. DOI: 10.1093/nar/gkad870.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023.

Nucleic Acids Res. 2022; 51(D1):D18-D28.

PMID: 36420893 PMC: 9825504. DOI: 10.1093/nar/gkac1073.

References

. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res. 2021; 50(D1):D27-D38. PMC: 8728233. DOI: 10.1093/nar/gkab951. View

Tian D, Wang P, Tang B, Teng X, Li C, Liu X . GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res. 2019; 48(D1):D927-D932. PMC: 6943065. DOI: 10.1093/nar/gkz828. View

Novichkov P, Ratnere I, Wolf Y, Koonin E, Dubchak I . ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res. 2008; 37(Database issue):D448-54. PMC: 2686458. DOI: 10.1093/nar/gkn684. View

Zdobnov E, Kuznetsov D, Tegenfeldt F, Manni M, Berkeley M, Kriventseva E . OrthoDB in 2020: evolutionary and functional annotations of orthologs. Nucleic Acids Res. 2020; 49(D1):D389-D393. PMC: 7779051. DOI: 10.1093/nar/gkaa1009. View

Li C, Tian D, Tang B, Liu X, Teng X, Zhao W . Genome Variation Map: a worldwide collection of genome variations across multiple species. Nucleic Acids Res. 2020; 49(D1):D1186-D1191. PMC: 7778933. DOI: 10.1093/nar/gkaa1005. View

Tulpan D, Leger S . The Plant Orthology Browser: An Orthology and Gene-Order Visualizer for Plant Comparative Genomics. Plant Genome. 2017; 10(1). DOI: 10.3835/plantgenome2016.08.0078. View

Shao Y, Chen C, Shen H, He B, Yu D, Jiang S . GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Res. 2019; 29(4):682-696. PMC: 6442393. DOI: 10.1101/gr.238733.118. View

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

Huerta-Cepas J, Szklarczyk D, Heller D, Hernandez-Plaza A, Forslund S, Cook H . eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2018; 47(D1):D309-D314. PMC: 6324079. DOI: 10.1093/nar/gky1085. View

10.

Nevers Y, Jones T, Jyothi D, Yates B, Ferret M, Portell-Silva L . The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 2022; 50(W1):W623-W632. PMC: 9252809. DOI: 10.1093/nar/gkac330. View

11.

Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L . Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. Plant J. 2017; 93(5):814-827. DOI: 10.1111/tpj.13804. View

12.

Galperin M, Wolf Y, Makarova K, Vera Alvarez R, Landsman D, Koonin E . COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2020; 49(D1):D274-D281. PMC: 7778934. DOI: 10.1093/nar/gkaa1018. View

13.

Kuzniar A, van Ham R, Pongor S, Leunissen J . The quest for orthologs: finding the corresponding gene across genomes. Trends Genet. 2008; 24(11):539-51. DOI: 10.1016/j.tig.2008.08.009. View

14.

Lu Q, Zhang M, Niu X, Wang S, Xu Q, Feng Y . Genetic variation and association mapping for 12 agronomic traits in indica rice. BMC Genomics. 2015; 16:1067. PMC: 4681178. DOI: 10.1186/s12864-015-2245-2. View

15.

Altenhoff A, Dessimoz C . Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol. 2009; 5(1):e1000262. PMC: 2612752. DOI: 10.1371/journal.pcbi.1000262. View

16.

Liao B, Zhang J . Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol. 2005; 23(3):530-40. DOI: 10.1093/molbev/msj054. View

17.

Wu H, Mao F, Olman V, Xu Y . Hierarchical classification of functionally equivalent genes in prokaryotes. Nucleic Acids Res. 2007; 35(7):2125-40. PMC: 1874638. DOI: 10.1093/nar/gkl1114. View

18.

Roth A, Gonnet G, Dessimoz C . Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics. 2008; 9:518. PMC: 2639434. DOI: 10.1186/1471-2105-9-518. View

19.

Kristensen D, Wolf Y, Mushegian A, Koonin E . Computational methods for Gene Orthology inference. Brief Bioinform. 2011; 12(5):379-91. PMC: 3178053. DOI: 10.1093/bib/bbr030. View

20.

Koonin E . Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005; 39:309-38. DOI: 10.1146/annurev.genet.39.073003.114725. View