Data Processing and Analysis for Protein Microarrays

  • David S. DeLuca
  • Ovidiu Marina
  • Surajit Ray
  • Guang Lan Zhang
  • Catherine J. Wu
  • Vladimir Brusic
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 723)

Abstract

Protein microarrays are a high-throughput technology capable of generating large quantities of proteomics data. They can be used for general research or for clinical diagnostics. Bioinformatics and statistical analysis techniques are required for interpretation and reaching biologically relevant conclusions from raw data. We describe essential algorithms for processing protein microarray data, including spot-finding on slide images, Z score, and significance analysis of microarrays (SAM) calculations, as well as the concentration dependent analysis (CDA). We also describe available tools for protein microarray analysis, and provide a template for a step-by-step approach to performing an analysis centered on the CDA method. We conclude with a discussion of fundamental and practical issues and considerations.

Key words

Protein microarray Concentration dependent analysis Z score Differential expression analysis Bioinformatics 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • David S. DeLuca
    • 1
  • Ovidiu Marina
    • 2
  • Surajit Ray
    • 3
  • Guang Lan Zhang
    • 4
  • Catherine J. Wu
    • 5
  • Vladimir Brusic
    • 1
  1. 1.Cancer Vaccine Center, Department of Medical OncologyDana-Farber Cancer InstituteBostonUSA
  2. 2.Department of Radiation OncologyWilliam Beaumont HospitalRoyal OakUSA
  3. 3.Department of Mathematics and StatisticsBoston UniversityBostonUSA
  4. 4.Cancer Vaccine Center, Department of Medical OncologyDana-Farber Cancer Institute, Harvard Medical SchoolBostonUSA
  5. 5.Division of Hematologic Neoplasia, Department of Medical Oncology, Cancer Vaccine CenterDana-Farber Cancer InstituteBostonUSA

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