A Nature Inspired Algorithm for Biclustering Microarray Data Analysis (PDF)

Research Paper (undergraduate) from the year 2015 in the subject Computer Science - Bioinformatics, grade: 1, Bannari Amman Institute of Technology, language: English, abstract: Extracting meaningful information from gene expression data poses a great challenge to the community of researchers in the field of computation as well as to biologists. It is possible to determine the behavioral patterns of genes such as nature of their interaction, similarity of their behavior and so on, through the analysis of gene expression data. If two different genes show similar expression patterns across the samples, this suggests a common pattern of regulation or relationship between their functions. These patterns have huge significance and application in bioinformatics and clinical research such as drug discovery, treatment planning, accurate diagnosis, prognosis, protein network analysis and so on.

In order to identify various patterns from gene expression data, data mining techniques are essential. Major data mining techniques which can be applied for the analysis of gene expression data include clustering, classification, association rule mining etc. Clustering is an important data mining technique for the analysis of gene expression data. However clustering has some disadvantages. To overcome the problems associated with clustering, biclustering is introduced. Clustering is a global model where as biclustering is a local model. Discovering such local expression patterns is essential for identifying many genetic pathways that are not apparent otherwise. It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.

Biclustering is a two dimensional clustering problem where we group the genes and samples simultaneously. It has a great potential in detecting marker genes that are associated with certain tissues or diseases. However, since the problem is NP-hard, there has been a lot of research in biclustering involving statistical and graph-theoretic. The proposed Cuckoo Search (CS) method finds the significant biclusters in large expression data. The experiment results are demonstrated on benchmark datasets. Also, this work determines the biological relevance of the biclusters with Gene Ontology in terms of function.