A proteome-scale map of the human interactome network.

Thomas Rolland, Murat Taşan, Benoit Charloteaux, Samuel J Pevzner, Quan Zhong, Nidhi Sahni, Song Yi, Irma Lemmens, Celia Fontanillo, Roberto Mosca, Atanas Kamburov, Susan D Ghiassian, Xinping Yang, Lila Ghamsari, Dawit Balcha, Bridget E Begg, Pascal Braun, Marc Brehme, Martin P Broly, Anne-Ruxandra Carvunis, Dan Convery-Zupan, Roser Corominas, Jasmin Coulombe-Huntington, Elizabeth Dann, Matija Dreze, Amélie Dricot, Changyu Fan, Eric Franzosa, Fana Gebreab, Bryan J Gutierrez, Madeleine F Hardy, Mike Jin, Shuli Kang, Ruth Kiros, Guan Ning Lin, Katja Luck, Andrew MacWilliams, Jörg Menche, Ryan R Murray, Alexandre Palagi, Matthew M Poulin, Xavier Rambout, John Rasla, Patrick Reichert, Viviana Romero, Elien Ruyssinck, Julie M Sahalie, Annemarie Scholz, Akash A Shah, Amitabh Sharma, Yun Shen, Kerstin Spirohn, Stanley Tam, Alexander O Tejeda, Shelly A Wanamaker, Jean-Claude Twizere, Kerwin Vega, Jennifer Walsh, Michael E Cusick, Yu Xia, Albert-László Barabási, Lilia M Iakoucheva, Patrick Aloy, Javier De Las Rivas, Jan Tavernier, Michael A Calderwood, David E Hill, Tong Hao, Frederick P Roth, Marc Vidal
Author Information
  1. Thomas Rolland: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  2. Murat Taşan: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
  3. Benoit Charloteaux: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  4. Samuel J Pevzner: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Boston University School of Medicine, Boston, MA 02118, USA.
  5. Quan Zhong: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
  6. Nidhi Sahni: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  7. Song Yi: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  8. Irma Lemmens: Department of Medical Protein Research, VIB, 9000 Ghent, Belgium.
  9. Celia Fontanillo: Cancer Research Center (Centro de Investigación del Cancer), University of Salamanca and Consejo Superior de Investigaciones Científicas, Salamanca 37008, Spain.
  10. Roberto Mosca: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain.
  11. Atanas Kamburov: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  12. Susan D Ghiassian: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA 02115, USA.
  13. Xinping Yang: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  14. Lila Ghamsari: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  15. Dawit Balcha: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  16. Bridget E Begg: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  17. Pascal Braun: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  18. Marc Brehme: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  19. Martin P Broly: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  20. Anne-Ruxandra Carvunis: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  21. Dan Convery-Zupan: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  22. Roser Corominas: Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
  23. Jasmin Coulombe-Huntington: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
  24. Elizabeth Dann: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  25. Matija Dreze: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  26. Amélie Dricot: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  27. Changyu Fan: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  28. Eric Franzosa: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
  29. Fana Gebreab: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  30. Bryan J Gutierrez: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  31. Madeleine F Hardy: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  32. Mike Jin: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  33. Shuli Kang: Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
  34. Ruth Kiros: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  35. Guan Ning Lin: Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
  36. Katja Luck: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  37. Andrew MacWilliams: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  38. Jörg Menche: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA 02115, USA.
  39. Ryan R Murray: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  40. Alexandre Palagi: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  41. Matthew M Poulin: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  42. Xavier Rambout: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Protein Signaling and Interactions Lab, GIGA-R, University of Liege, 4000 Liege, Belgium.
  43. John Rasla: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  44. Patrick Reichert: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  45. Viviana Romero: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  46. Elien Ruyssinck: Department of Medical Protein Research, VIB, 9000 Ghent, Belgium.
  47. Julie M Sahalie: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  48. Annemarie Scholz: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  49. Akash A Shah: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  50. Amitabh Sharma: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA 02115, USA.
  51. Yun Shen: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  52. Kerstin Spirohn: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  53. Stanley Tam: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  54. Alexander O Tejeda: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  55. Shelly A Wanamaker: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  56. Jean-Claude Twizere: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Protein Signaling and Interactions Lab, GIGA-R, University of Liege, 4000 Liege, Belgium.
  57. Kerwin Vega: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  58. Jennifer Walsh: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  59. Michael E Cusick: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  60. Yu Xia: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada.
  61. Albert-László Barabási: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  62. Lilia M Iakoucheva: Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
  63. Patrick Aloy: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
  64. Javier De Las Rivas: Cancer Research Center (Centro de Investigación del Cancer), University of Salamanca and Consejo Superior de Investigaciones Científicas, Salamanca 37008, Spain.
  65. Jan Tavernier: Department of Medical Protein Research, VIB, 9000 Ghent, Belgium.
  66. Michael A Calderwood: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  67. David E Hill: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  68. Tong Hao: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
  69. Frederick P Roth: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Canadian Institute for Advanced Research, Toronto M5G 1Z8, Canada. Electronic address: fritz.roth@utoronto.ca.
  70. Marc Vidal: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: marc_vidal@dfci.harvard.edu.

Abstract

Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ?30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a "broader" human interactome network than currently appreciated. The map also uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help "connect the dots" of the genomic revolution.

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Grants

  1. P50HG004233/NHGRI NIH HHS
  2. R01 HG001715/NHGRI NIH HHS
  3. R01 MH091350/NIMH NIH HHS
  4. U01HL108630/NHLBI NIH HHS
  5. R33CA132073/NCI NIH HHS
  6. P50 HG004233/NHGRI NIH HHS
  7. R21 MH104766/NIMH NIH HHS
  8. R33 CA132073/NCI NIH HHS
  9. R01MH105524/NIMH NIH HHS
  10. U01HG001715/NHGRI NIH HHS
  11. U01 HL098166/NHLBI NIH HHS
  12. RC4HG006066/NHGRI NIH HHS
  13. RC4 HG006066/NHGRI NIH HHS
  14. U01 HL108630/NHLBI NIH HHS
  15. R01 HD065288/NICHD NIH HHS
  16. 340941/European Research Council
  17. U54CA112962/NCI NIH HHS
  18. U01 HG001715/NHGRI NIH HHS
  19. R21MH104766/NIMH NIH HHS
  20. R01 MH105524/NIMH NIH HHS
  21. U01HL098166/NHLBI NIH HHS
  22. R01MH091350/NIMH NIH HHS
  23. R01HD065288/NICHD NIH HHS
  24. U54 CA112962/NCI NIH HHS

MeSH Term

Animals
Databases, Protein
Genome-Wide Association Study
Humans
Mice
Neoplasms
Protein Interaction Maps
Proteome

Chemicals

Proteome

Word Cloud

Created with Highcharts 10.0.0maphumaninteractomereferencewillsystematichigh-qualityavailablecurrentlynetworkcancerJustgenomesequencesrevolutionizedgeneticsmapsnetworkscriticalfullyunderstandgenotype-phenotyperelationshipsdescribe?14000binaryprotein-proteininteractionsequalquality?30%largersmall-scalestudiespublishedliteraturelastdecadesinformationhighlybiasedcoversrelativelysmallportionproteomeappearsstrikinglyhomogeneousrevealing"broader"appreciatedalsouncoverssignificantinterconnectivityknowncandidategeneproductsprovidingunbiasedevidenceexpandedfunctionallandscapedemonstratingmodelshelp"connectdots"genomicrevolutionproteome-scale

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