Design and Implementation of an Analytical Module for a Microarray Database

Student: Anthony D Percival

Supervisor: J Hallinan

Category: Computer Systems Engineering Thesis Project

The gathering and analysis of gene expression data from DNA microarrays plays an important role in modern biotechnology. The design and implementation of a web server analytic module that is capable of storing and analysing large data sets resulting from DNA microarrays was investigated.

The module is coded in PostgreSQL and interfaced using HTML and the scripting language PHP. The data analysis is performed by J-Express, a Java application that allows the user to analyse gene expression data. The raw data used for testing is based on the data from Stanford University’s NCI60 Cancer Microarray Project.

The resulting analytic module is capable of performing five different analytic techniques on the data set: Hierarchical Clustering, Self Organising maps, K-Means Clustering, Principal Component Analysis and Profile Similarity Search. This module is an extension on Stanford University’s GeneExplorer application, which is only capable of performing Hierarchical Clustering analysis.

Poster Presentation (PDF)

Thesis Document (PDF)