BrainBase: a curated knowledgebase for brain diseases.

Lin Liu, Yang Zhang, Guangyi Niu, Qianpeng Li, Zhao Li, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Tianyi Xu, Ruru Chen, Xufei Teng, Rongqin Zhang, Dong Zou, Lina Ma, Zhang Zhang
Author Information
  1. Lin Liu: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. ORCID
  2. Yang Zhang: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  3. Guangyi Niu: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  4. Qianpeng Li: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  5. Zhao Li: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  6. Tongtong Zhu: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  7. Changrui Feng: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. ORCID
  8. Xiaonan Liu: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  9. Yuansheng Zhang: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  10. Tianyi Xu: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  11. Ruru Chen: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  12. Xufei Teng: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  13. Rongqin Zhang: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  14. Dong Zou: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
  15. Lina Ma: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. ORCID
  16. Zhang Zhang: National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. ORCID

Abstract

Brain is the central organ of the nervous system and any brain disease can seriously affect human health. Here we present BrainBase (https://ngdc.cncb.ac.cn/brainbase), a curated knowledgebase for brain diseases that aims to provide a whole picture of brain diseases and associated genes. Specifically, based on manual curation of 2768 published articles along with information retrieval from several public databases, BrainBase features comprehensive collection of 7175 disease-gene associations spanning a total of 123 brain diseases and linking with 5662 genes, 16 591 drug-target interactions covering 2118 drugs/chemicals and 623 genes, and five types of specific genes in light of expression specificity in brain tissue/regions/cerebrospinal fluid/cells. In addition, considering the severity of glioma among brain tumors, the current version of BrainBase incorporates 21 multi-omics datasets, presents molecular profiles across various samples/conditions and identifies four groups of glioma featured genes with potential clinical significance. Collectively, BrainBase integrates not only valuable curated disease-gene associations and drug-target interactions but also molecular profiles through multi-omics data analysis, accordingly bearing great promise to serve as a valuable knowledgebase for brain diseases.

References

  1. Annu Rev Biochem. 2010;79:321-49 [PMID: 20192758]
  2. Arch Med Sci. 2015 Dec 10;11(6):1164-78 [PMID: 26788077]
  3. N Engl J Med. 2005 Mar 10;352(10):997-1003 [PMID: 15758010]
  4. Acta Neuropathol. 2007 Aug;114(2):97-109 [PMID: 17618441]
  5. Cancer Cells. 1991 Jun;3(6):221-6 [PMID: 1654969]
  6. Methods Mol Biol. 2016;1418:93-110 [PMID: 27008011]
  7. Nature. 2018 Mar 22;555(7697):469-474 [PMID: 29539639]
  8. Cell. 2013 Oct 10;155(2):462-77 [PMID: 24120142]
  9. Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7 [PMID: 21948594]
  10. PLoS One. 2012;7(6):e40262 [PMID: 22768266]
  11. Methods Mol Biol. 2013;1015:311-20 [PMID: 23824865]
  12. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6 [PMID: 18048412]
  13. PLoS Biol. 2018 Nov 26;16(11):e3000066 [PMID: 30475794]
  14. Am J Med Genet A. 2014 Jun;164A(6):1503-11 [PMID: 24700709]
  15. Nucleic Acids Res. 2019 Jan 8;47(D1):D1013-D1017 [PMID: 30364956]
  16. Sci Rep. 2013 Dec 10;3:3467 [PMID: 24322672]
  17. Sci Rep. 2018 Jun 11;8(1):8868 [PMID: 29892006]
  18. Neuron. 2016 Nov 2;92(3):574-581 [PMID: 27809997]
  19. Acta Neuropathol. 2013 Sep;126(3):443-51 [PMID: 23904111]
  20. BMJ. 2020 Oct 9;371:m3683 [PMID: 33037002]
  21. Int J Biol Macromol. 2021 Mar 31;174:263-269 [PMID: 33529633]
  22. Acta Pharm Sin B. 2020 Aug;10(8):1347-1359 [PMID: 32963936]
  23. Nucleic Acids Res. 2019 Jan 8;47(D1):D128-D134 [PMID: 30329098]
  24. Front Genet. 2019 Nov 29;10:1202 [PMID: 31850066]
  25. Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6 [PMID: 22080554]
  26. Cancer Cell. 2010 Jan 19;17(1):98-110 [PMID: 20129251]
  27. Nucleic Acids Res. 2023 Jan 6;51(D1):D18-D28 [PMID: 36420893]
  28. Neuron. 2016 Nov 2;92(3):591-596 [PMID: 27809999]
  29. Sci Rep. 2019 May 10;9(1):7233 [PMID: 31076736]
  30. Science. 2018 May 11;360(6389):660-663 [PMID: 29748285]
  31. Nucleic Acids Res. 2021 Jan 8;49(D1):D1138-D1143 [PMID: 33068428]
  32. Nucleic Acids Res. 2019 Jan 8;47(D1):D786-D792 [PMID: 30304474]
  33. Biol Direct. 2020 Jun 15;15(1):10 [PMID: 32539851]
  34. Neurochem Res. 2020 Feb;45(2):508-518 [PMID: 31939089]
  35. J Neurosci. 2017 Apr 12;37(15):4103-4116 [PMID: 28292834]
  36. PLoS Comput Biol. 2010 Feb 05;6(2):e1000662 [PMID: 20140234]
  37. Nucleic Acids Res. 2021 Jan 8;49(D1):D1029-D1037 [PMID: 32976581]
  38. Neuropsychopharmacol Rep. 2020 Jun;40(2):201-205 [PMID: 32426945]
  39. J Pathol Transl Med. 2017 May;51(3):205-223 [PMID: 28535583]
  40. Nucleic Acids Res. 2019 Jan 8;47(D1):D78-D83 [PMID: 30357418]
  41. Cell. 2017 Nov 30;171(6):1437-1452.e17 [PMID: 29195078]
  42. Protein Sci. 2018 Jan;27(1):233-244 [PMID: 28940711]
  43. Genomics Proteomics Bioinformatics. 2021 Feb;19(1):1-12 [PMID: 33662628]
  44. Bioinformatics. 2007 Jun 1;23(11):1348-55 [PMID: 17384019]
  45. BMC Bioinformatics. 2015;16 Suppl 5:S1 [PMID: 25861037]
  46. Nucleic Acids Res. 2019 Jan 8;47(D1):D721-D728 [PMID: 30289549]
  47. Neuro Oncol. 2017 Jan;19(1):139-141 [PMID: 28031383]
  48. Cell. 2018 Apr 5;173(2):283-285 [PMID: 29625045]
  49. Nat Genet. 2013 Jun;45(6):580-5 [PMID: 23715323]
  50. Cell. 2016 Jan 28;164(3):550-63 [PMID: 26824661]
  51. Signal Transduct Target Ther. 2019 Oct 12;4:42 [PMID: 31637020]
  52. Bioinformatics. 2005 Mar 1;21(5):650-9 [PMID: 15388519]
  53. Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012 [PMID: 30445434]
  54. Nat Clin Pract Neurol. 2006 Sep;2(9):494-503; quiz 1 p following 516 [PMID: 16932614]
  55. Hum Mol Genet. 2017 Jan 1;26(1):44-51 [PMID: 28031287]
  56. Philos Trans R Soc Lond B Biol Sci. 2015 May 19;370(1668): [PMID: 25823872]
  57. Clin Transl Med. 2018 Jan 17;7(1):3 [PMID: 29340951]
  58. Oncogene. 2008 Jun 5;27(25):3587-95 [PMID: 18212741]
  59. Cell Mol Life Sci. 2018 Feb;75(3):385-402 [PMID: 28821904]
  60. Cancer Biol Ther. 2013 Apr;14(4):287-94 [PMID: 23358475]
  61. Brief Bioinform. 2021 Nov 5;22(6): [PMID: 34086851]
  62. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):253-8 [PMID: 12506194]
  63. Nucleic Acids Res. 2019 Jan 8;47(D1):D983-D988 [PMID: 30364969]

MeSH Term

Brain Diseases
Computational Biology
Databases, Genetic
Glioma
Humans
Knowledge Bases

Links to CNCB-NGDC Resources

Database Commons: DBC007427 (BrainBase)

Word Cloud

Created with Highcharts 10.0.0braindiseasesgenesBrainBasecuratedknowledgebasedisease-geneassociationsdrug-targetinteractionsgliomamulti-omicsmolecularprofilesvaluableBraincentralorgannervoussystemdiseasecanseriouslyaffecthumanhealthpresenthttps://ngdccncbaccn/brainbaseaimsprovidewholepictureassociatedSpecificallybasedmanualcuration2768publishedarticlesalonginformationretrievalseveralpublicdatabasesfeaturescomprehensivecollection7175spanningtotal123linking566216591covering2118drugs/chemicals623fivetypesspecificlightexpressionspecificitytissue/regions/cerebrospinalfluid/cellsadditionconsideringseverityamongtumorscurrentversionincorporates21datasetspresentsacrossvarioussamples/conditionsidentifiesfourgroupsfeaturedpotentialclinicalsignificanceCollectivelyintegratesalsodataanalysisaccordinglybearinggreatpromiseserveBrainBase:

Similar Articles

Cited By (5)