Effective Feature Selection for Classification of Promoter Sequences

• Published in: PloS one Vol. 11; no. 12; p. e0167165
• Main Authors: K, Kouser, P G, Lavanya, Rangarajan, Lalitha, K, Acharya Kshitish
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 15.12.2016; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Artificial intelligence; Bioinformatics; Biology and Life Sciences; Classification; Computation; Computational Biology - methods; Computer and Information Sciences; Computer applications; Computer science; Data mining; Decision trees; Deoxyribonucleic acid; DNA; DNA sequencing; Engineering and Technology; Functional analysis; Gene expression; Gene Expression Regulation; Gene regulation; Gene sequencing; Genetic transformation; Models, Genetic; Nucleotide sequence; Nucleotides; Physical Sciences; Promoter Regions, Genetic; Promoters; Protein binding; Proteins; Pyridine nucleotide reductase; Regulatory mechanisms (biology); Research and Analysis Methods; Support vector machines; Transcription factors; Transformation; India
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0167165

Exploring novel computational methods in making sense of biological data has not only been a necessity, but also productive. A part of this trend is the search for more efficient in silico methods/tools for analysis of promoters, which are parts of DNA sequences that are involved in regulation of expression of genes into other functional molecules. Promoter regions vary greatly in their function based on the sequence of nucleotides and the arrangement of protein-binding short-regions called motifs. In fact, the regulatory nature of the promoters seems to be largely driven by the selective presence and/or the arrangement of these motifs. Here, we explore computational classification of promoter sequences based on the pattern of motif distributions, as such classification can pave a new way of functional analysis of promoters and to discover the functionally crucial motifs. We make use of Position Specific Motif Matrix (PSMM) features for exploring the possibility of accurately classifying promoter sequences using some of the popular classification techniques. The classification results on the complete feature set are low, perhaps due to the huge number of features. We propose two ways of reducing features. Our test results show improvement in the classification output after the reduction of features. The results also show that decision trees outperform SVM (Support Vector Machine), KNN (K Nearest Neighbor) and ensemble classifier LibD3C, particularly with reduced features. The proposed feature selection methods outperform some of the popular feature transformation methods such as PCA and SVD. Also, the methods proposed are as accurate as MRMR (feature selection method) but much faster than MRMR. Such methods could be useful to categorize new promoters and explore regulatory mechanisms of gene expressions in complex eukaryotic species.