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Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering

  • Mehmet Deveci
  • Onur Küçüktunç
  • Kemal Eren
  • Doruk Bozdağ
  • Kamer Kaya
  • Ümit V. ÇatalyürekEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1375)

Abstract

Rapid development and increasing popularity of gene expression microarrays have resulted in a number of studies on the discovery of co-regulated genes. One important way of discovering such co-regulations is the query-based search since gene co-expressions may indicate a shared role in a biological process. Although there exist promising query-driven search methods adapting clustering, they fail to capture many genes that function in the same biological pathway because microarray datasets are fraught with spurious samples or samples of diverse origin, or the pathways might be regulated under only a subset of samples. On the other hand, a class of clustering algorithms known as biclustering algorithms which simultaneously cluster both the items and their features are useful while analyzing gene expression data, or any data in which items are related in only a subset of their samples. This means that genes need not be related in all samples to be clustered together. Because many genes only interact under specific circumstances, biclustering may recover the relationships that traditional clustering algorithms can easily miss. In this chapter, we briefly summarize the literature using biclustering for querying co-regulated genes. Then we present a novel biclustering approach and evaluate its performance by a thorough experimental analysis.

Keywords:

Biclustering Microarray Gene expression Clustering 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Mehmet Deveci
    • 1
  • Onur Küçüktunç
    • 1
  • Kemal Eren
    • 1
  • Doruk Bozdağ
    • 2
  • Kamer Kaya
    • 3
  • Ümit V. Çatalyürek
    • 4
    Email author
  1. 1.Computer Science and EngineeringThe Ohio State UniversityColumbusUSA
  2. 2.Biomedical InformaticsThe Ohio State UniversityColumbusUSA
  3. 3.Computer Science and EngineeringSabancı UniversityIstanbulTurkey
  4. 4.Biomedical Informatics, Department of Electrical and Computer EngineeringThe Ohio State UniversityColumbusUSA

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