Title
Scatter search-based identification of local patterns with positive and negative correlations in gene expression data
Date Issued
27 July 2015
Access level
open access
Resource Type
journal article
Author(s)
Pablo de Olavide University
Publisher(s)
Elsevier Ltd
Abstract
This paper presents a scatter search approach based on linear correlations among genes to find biclusters, which include both shifting and scaling patterns and negatively correlated patterns contrarily to most of correlation-based algorithms published in the literature. The methodology established here for comparison is based on a priori biological information stored in the well-known repository Gene Ontology (GO). In particular, the three existing categories in GO, Biological Process, Cellular Components and Molecular Function, have been used. The performance of the proposed algorithm has been compared to other benchmark biclustering algorithms, specifically a group of classical biclustering algorithms and two algorithms that use correlation-based merit functions. The proposed algorithm outperforms the benchmark algorithms and finds patterns based on negative correlations. Although these patterns contain important relationship among genes, they are not found by most of biclustering algorithms. The experimental study also shows the importance of the size in a bicluster in addition to the value of its correlation. In particular, the size of a bicluster has an influence over its enrichment in a GO term.
Start page
637
End page
651
Volume
35
Language
English
OCDE Knowledge area
Biología celular, Microbiología
Genética, Herencia
Subjects
Scopus EID
2-s2.0-84937805065
Source
Applied Soft Computing Journal
ISSN of the container
15684946
Sponsor(s)
We would like to thank Spanish Ministry of Science and Innovation , Junta de Andalucía and University Pablo de Olavide for the financial support under projects TIN2011-28956-C02-00 , P12-TIC-1728 and APPB813097 , respectively.
Sources of information:
Directorio de Producción Científica
Scopus