Data Processing and Analysis for Protein Microarrays

David S. DeLuca, Ovidiu Marina, Surajit Ray, Guang Lan Zhang, Catherine J. Wu, Vladimir Brusic

Research output: Chapter in Book/Conference proceedingBook Chapterpeer-review

12 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages337-347
Number of pages11
DOIs
Publication statusPublished - 2011
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume723
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Bioinformatics
  • Concentration dependent analysis
  • Differential expression analysis
  • Protein microarray
  • Z score

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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