Direct integration of microarrays for selecting informative genes and phenotype classification

Youngmi Yoon, Jongchan Lee, Sanghyun Park, Sangjay Bien, Hyun Cheol Chung, Sun Young Rha

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


The ability to provide thousands of gene expression values simultaneously makes microarray data very useful for phenotype classification. A major constraint in phenotype classification is that the number of genes greatly exceeds the number of samples. We overcame this constraint in two ways; we increased the number of samples by integrating independently generated microarrays that had been designed with the same biological objectives, and reduced the number of genes involved in the classification by selecting a small set of informative genes. We were able to maximally use the abundant microarray data that is being stockpiled by thousands of different research groups while improving classification accuracy. Our goal is to implement a feature (gene) selection method that can be applicable to integrated microarrays as well as to build a highly accurate classifier that permits straightforward biological interpretation. In this paper, we propose a two-stage approach. Firstly, we performed a direct integration of individual microarrays by transforming an expression value into a rank value within a sample and identified informative genes by calculating the number of swaps to reach a perfectly split sequence. Secondly, we built a classifier which is a parameter-free ensemble method using only the pre-selected informative genes. By using our classifier that was derived from large, integrated microarray sample datasets, we achieved high accuracy, sensitivity, and specificity in the classification of an independent test dataset.

Original languageEnglish
Pages (from-to)88-105
Number of pages18
JournalInformation sciences
Issue number1
Publication statusPublished - 2008 Jan 2

Bibliographical note

Funding Information:
This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MOST) (No. R01-2006-000-11106-0).

All Science Journal Classification (ASJC) codes

  • Software
  • Control and Systems Engineering
  • Theoretical Computer Science
  • Computer Science Applications
  • Information Systems and Management
  • Artificial Intelligence


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