Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans (original) (raw)

  1. Suraj Peri1,4,16,
  2. J. Daniel Navarro1,5,16,
  3. Ramars Amanchy1,
  4. Troels Z. Kristiansen1,4,
  5. Chandra Kiran Jonnalagadda1,6,
  6. Vineeth Surendranath6,
  7. Vidya Niranjan6,
  8. Babylakshmi Muthusamy6,
  9. T.K.B. Gandhi6,
  10. Mads Gronborg1,4,
  11. Nieves Ibarrola1,
  12. Nandan Deshpande6,
  13. K. Shanker6,
  14. H.N. Shivashankar6,
  15. B.P. Rashmi6,
  16. M.A. Ramya6,
  17. Zhixing Zhao1,
  18. K.N. Chandrika6,
  19. N. Padma6,
  20. H.C. Harsha6,
  21. A.J. Yatish6,
  22. M.P. Kavitha6,
  23. Minal Menezes6,
  24. Dipanwita Roy Choudhury6,
  25. Shubha Suresh6,
  26. Neelanjana Ghosh6,
  27. R. Saravana6,
  28. Sreenath Chandran6,
  29. Subhalakshmi Krishna6,
  30. Mary Joy6,
  31. Sanjeev K. Anand6,
  32. V. Madavan6,
  33. Ansamma Joseph6,
  34. Guang W. Wong7,
  35. William P. Schiemann8,
  36. Stefan N. Constantinescu9,
  37. Lily Huang7,
  38. Roya Khosravi-Far10,
  39. Hanno Steen11,
  40. Muneesh Tewari12,
  41. Saghi Ghaffari13,
  42. Gerard C. Blobe14,
  43. Chi V. Dang2,
  44. Joe G.N. Garcia2,
  45. Jonathan Pevsner3,
  46. Ole N. Jensen4,
  47. Peter Roepstorff4,
  48. Krishna S. Deshpande6,
  49. Arul M. Chinnaiyan15,
  50. Ada Hamosh1,
  51. Aravinda Chakravarti1, and
  52. Akhilesh Pandey1,17
  53. 1 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
  54. 2 Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
  55. 3 Kennedy Krieger Research Institute, Johns Hopkins University, Baltimore, Maryland 21287, USA
  56. 4 Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
  57. 5 División de Hepatología y Terapia génica, Unidad de Proteómica, CIMA, Universidad de Navarra, 31008 Pamplona, Spain
  58. 6 Institute of Bioinformatics, International Technology Park Ltd., Bangalore 560 066, India
  59. 7 Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
  60. 8 National Jewish Medical and Research Center, Denver, Colorado 80202, USA
  61. 9 Ludwig Institute for Cancer Research, Brussels, Belgium
  62. 10 Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA
  63. 11 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215, USA
  64. 12 Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
  65. 13 Mount Sinai School of Medicine, New York, New York 10029, USA
  66. 14 Pharmacology and Cancer Biology program, Duke University, Durham, North Carolina 27710, USA
  67. 15 Departments of Pathology and Urology, University of Michigan, Ann Arbor, Michigan 48109, USA

Abstract

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

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