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01 06, 2023;51 (D1): D994-D1002.

HGD: an integrated homologous gene database across multiple species.

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
Author Information
  1. Guangya Duan: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  2. Gangao Wu: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  3. Xiaoning Chen: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  4. Dongmei Tian: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  5. Zhaohua Li: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  6. Yanling Sun: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  7. Zhenglin Du: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  8. Lili Hao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  9. Shuhui Song: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  10. Yuan Gao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  11. Jingfa Xiao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  12. Zhang Zhang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  13. Yiming Bao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  14. Bixia Tang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  15. Wenming Zhao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
PMID: 36318261 DOI: 10.1093/nar/gkac970

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.

References

  1. Nucleic Acids Res. 2022 Jan 7;50(D1):D27-D38 [PMID: 34718731]
  2. Nucleic Acids Res. 2020 Jan 8;48(D1):D927-D932 [PMID: 31566222]
  3. Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54 [PMID: 18845571]
  4. Nucleic Acids Res. 2021 Jan 8;49(D1):D389-D393 [PMID: 33196836]
  5. Nucleic Acids Res. 2021 Jan 8;49(D1):D1186-D1191 [PMID: 33170268]
  6. Plant Genome. 2017 Mar;10(1): [PMID: 28464063]
  7. Genome Res. 2019 Apr;29(4):682-696 [PMID: 30862647]
  8. J Mol Biol. 1990 Oct 5;215(3):403-10 [PMID: 2231712]
  9. Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314 [PMID: 30418610]
  10. Nucleic Acids Res. 2022 May 12;: [PMID: 35552456]
  11. Plant J. 2018 Mar;93(5):814-827 [PMID: 29265542]
  12. Nucleic Acids Res. 2021 Jan 8;49(D1):D274-D281 [PMID: 33167031]
  13. Trends Genet. 2008 Nov;24(11):539-51 [PMID: 18819722]
  14. BMC Genomics. 2015 Dec 16;16:1067 [PMID: 26673149]
  15. PLoS Comput Biol. 2009 Jan;5(1):e1000262 [PMID: 19148271]
  16. Mol Biol Evol. 2006 Mar;23(3):530-40 [PMID: 16280543]
  17. Nucleic Acids Res. 2007;35(7):2125-40 [PMID: 17353185]
  18. BMC Bioinformatics. 2008 Dec 04;9:518 [PMID: 19055798]
  19. Brief Bioinform. 2011 Sep;12(5):379-91 [PMID: 21690100]
  20. Annu Rev Genet. 2005;39:309-38 [PMID: 16285863]
  21. Biochimie. 2008 Apr;90(4):595-608 [PMID: 17961904]
  22. Gene. 2012 Jan 15;492(1):199-211 [PMID: 22056699]
  23. PLoS One. 2015 Mar 18;10(3):e0119873 [PMID: 25785447]
  24. Genome Biol. 2005;6(5):R44 [PMID: 15892872]
  25. Bioessays. 2008 Jul;30(7):653-8 [PMID: 18536034]
  26. Genome Biol. 2016 Jun 06;17(1):122 [PMID: 27268795]
  27. Genome Res. 2009 Feb;19(2):327-35 [PMID: 19029536]
  28. Genome Biol. 2009;10(9):403 [PMID: 19785718]
  29. Mol Biol Evol. 2021 Jul 29;38(8):3033-3045 [PMID: 33822172]
  30. Protein Sci. 2000 Dec;9(12):2344-53 [PMID: 11206056]
  31. Nat Rev Genet. 2013 May;14(5):360-6 [PMID: 23552219]
  32. Trends Genet. 2009 May;25(5):210-6 [PMID: 19368988]
  33. Nucleic Acids Res. 2017 Jan 4;45(D1):D687-D690 [PMID: 27742821]
  34. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D173-80 [PMID: 16381840]
  35. BMC Bioinformatics. 2011 Aug 31;12:357 [PMID: 21880147]
  36. Front Plant Sci. 2015 Jul 21;6:536 [PMID: 26257749]
  37. Sci Rep. 2020 Jan 20;10(1):683 [PMID: 31959799]
  38. Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334 [PMID: 33290552]
  39. Plant J. 2017 Feb;89(4):805-824 [PMID: 27859855]
  40. Genetics. 2010 Feb;184(2):343-50 [PMID: 19933874]
  41. Plant Cell Environ. 2018 Apr;41(4):721-736 [PMID: 29094353]
  42. Nucleic Acids Res. 2021 Jan 8;49(D1):D373-D379 [PMID: 33174605]
  43. Nucleic Acids Res. 2014 Jan;42(Database issue):D922-5 [PMID: 24194607]
  44. Nucleic Acids Res. 2018 Jan 4;46(D1):D1168-D1180 [PMID: 29186578]
  45. Nucleic Acids Res. 2015 Jan;43(Database issue):D234-9 [PMID: 25429972]
  46. Nucleic Acids Res. 2022 Jan 7;50(D1):D1016-D1024 [PMID: 34591957]
  47. Syst Zool. 1970 Jun;19(2):99-113 [PMID: 5449325]
  48. Nucleic Acids Res. 2020 Jan 8;48(D1):D650-D658 [PMID: 31552413]
  49. Front Plant Sci. 2021 Oct 05;12:743838 [PMID: 34675951]
  50. Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489 [PMID: 33237286]
  51. J Exp Zool B Mol Dev Evol. 2003 Oct 15;299(1):9-17 [PMID: 14508812]
  52. Nucleic Acids Res. 2022 Jan 7;50(D1):D1255-D1261 [PMID: 34755882]
  53. Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995 [PMID: 34791404]
  54. Nucleic Acids Res. 2021 Jan 8;49(D1):D394-D403 [PMID: 33290554]
  55. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45 [PMID: 26553804]
  56. BMC Genomics. 2009 Dec 23;10:630 [PMID: 20030836]

MeSH Term

Animals
Databases, Genetic
Molecular Sequence Annotation
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC008199 (HGD)

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