A practical question based on cross-platform microarray data normalization: Are BOEC more like large vessel or microvascular endothelial cells or neither of them?

Axiang Jiang, Wei Pan, Liming C. Milbauer, Yu Shyr, Robert P Hebbel

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

Since the available microarray data of BOEC (human blood outgrowth endothelial cells), large vessel, and microvascular endothelial cells were from two different platforms, a working cross-platform normalization method was needed to make these data comparable. With six HUVEC (human umbilical vein endothelial cells) samples hybridized on two-channel cDNA arrays and six HUVEC samples on Affymetrix arrays, 64 possible combinations of a three-step normalization procedure were investigated to search for the best normalization method, which was selected, based on two criteria measuring the extent to which expression profiles of biological samples of the same cell type arrayed on two platforms were indistinguishable. Next, three discriminative gene lists between the large vessel and the microvascular endothelial cells were achieved by SAM (significant analysis of microarrays), PAM (prediction analysis for microarrays), and a combination of SAM and PAM lists. The final discriminative gene list was selected by SVM (support vector machine). Based on this discriminative gene list, SVM classification analysis with best tuning parameters and 10,000 times of validations showed that BOEC were far from large vessel cells, they either formed their own class, or fell into the microvascular class. Based on all the common genes between the two platforms, SVM analysis further confirmed this conclusion.

Original languageEnglish (US)
Pages (from-to)875-893
Number of pages19
JournalJournal of Bioinformatics and Computational Biology
Volume5
Issue number4
DOIs
StatePublished - Aug 2007

Bibliographical note

Funding Information:
We thank Dr. William C. Aird’s Program Project Grant, funded by NIH/NHLBI P01 grant HL076540, and Dr. Jamie Topper from Millennium for supporting this research.

Keywords

  • BOEC
  • Classification
  • Cross platform
  • Large vessel endothelial cells
  • Microarray
  • Microvascular endothelial cells
  • Normalization
  • Support vector machine
  • Validation

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