Assessment of clustering algorithms for unsupervised transcription factor binding site discovery


Karabulut M., İBRİKÇİ T.

EXPERT SYSTEMS WITH APPLICATIONS, cilt.38, ss.11160-11166, 2011 (SCI İndekslerine Giren Dergi) identifier identifier

  • Cilt numarası: 38 Konu: 9
  • Basım Tarihi: 2011
  • Doi Numarası: 10.1016/j.eswa.2011.02.161
  • Dergi Adı: EXPERT SYSTEMS WITH APPLICATIONS
  • Sayfa Sayısı: ss.11160-11166

Özet

Identification of transcription factor binding sites is a key task to understand gene regulation mechanism to discover gene networks and functions. Clustering approach is proved to be useful when finding such patterns residing in promoter regions of co-regulated genes. Four clustering algorithms, Self-Organizing Map, K-Means, Fuzzy C-Means and Expectation-Maximization are studied in this paper to discover motifs in datasets extracted from Saccharomyces cerevisiae, Escherichia coli, Droshophila melanogaster and Homo sapiens DNA sequences. Required modifications to clustering algorithms in order to adapt them to motif finding task are presented through the paper. Then, their motif-finding performances are discussed carefully and evaluated against a popular motif-finding method, MEME. (C) 2011 Elsevier Ltd. All rights reserved.