347
Views
6
CrossRef citations to date
0
Altmetric
Editorial

Protein set analyses: how could this impact the clinic?

Pages 305-307 | Published online: 09 Jan 2014

References

  • Weinberg R. Point: hypotheses first. Nature 464(7289), 678 (2010).
  • Zuk O, Hechter E, Sunyaev SR, Lander ES. The mystery of missing heritability: Genetic interactions create phantom heritability. Proc. Natl Acad. Sci. USA 109(4), 1193–1198 (2012).
  • Feldmann R, Fischer C, Kodelja V et al. Genome-wide analysis of LXRalpha activation reveals new transcriptional networks in human atherosclerotic foam cells. Nucleic Acids Res. 41(6), 3518–3531 (2013).
  • Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science 339(6127), 1546–1558 (2013).
  • Forbes SA, Bindal N, Bamford S et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39(Database issue), D945–D950 (2011).
  • Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc. Natl Acad. Sci. USA 104(21), 8685–8690 (2007).
  • Grueneberg DA, Degot S, Pearlberg J et al. Kinase requirements in human cells: I. Comparing kinase requirements across various cell types. Proc. Natl Acad. Sci. USA 105(43), 16472–16477 (2008).
  • Weeks DE, Lathrop GM. Polygenic disease: methods for mapping complex disease traits. Trends Genet. 11(12), 513–519 (1995).
  • Sauer S, Lange BM, Gobom J, Nyarsik L, Seitz H, Lehrach H. Miniaturization in functional genomics and proteomics. Nat. Rev. Genet. 6(6), 465–476 (2005).
  • Kliem M, Sauer S. The essence on mass spectrometry based microbial diagnostics. Curr. Opin. Microbiol. 15(3), 397–402 (2012).
  • Sauer S, Freiwald A, Maier T et al. Classification and identification of bacteria by mass spectrometry and computational analysis. PLoS ONE 3(7), e2843 (2008).
  • Freiwald A, Mao L, Kodelja V et al. Differential analysis of Crohn's disease and ulcerative colitis by mass spectrometry. Inflamm. Bowel Dis. 17(4), 1051–1052 (2011).
  • Baumann S, Ceglarek U, Fiedler GM, Lembcke J, Leichtle A, Thiery J. Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 51(6), 973–980 (2005).
  • Meierhofer D, Weidner C, Hartmann L et al. Protein sets define disease states and predict in vivo effects of drug treatment. Mol. Cell Proteomics 12(7), 1965–1979 (2013).
  • Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics 10(6), 1316–1327 (2010).
  • Cha S, Imielinski MB, Rejtar T et al. In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol. Cell Proteomics 9(11), 2529–2544 (2010).
  • Subramanian A, Tamayo P, Mootha VK et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102(43), 15545–15550 (2005).
  • Weidner C, de Groot JC, Prasad A et al. Amorfrutins are potent antidiabetic dietary natural products. Proc. Natl Acad. Sci. USA 109(19), 7257–7262 (2012).
  • Michalski A, Damoc E, Hauschild JP et al. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell Proteomics 10(9), M111.011015 (2011).
  • Mann M, Kelleher NL. Precision proteomics: the case for high resolution and high mass accuracy. Proc. Natl Acad. Sci. USA 105(47), 18132–18138 (2008).

Website

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.