Abstract
BackgroundMicroarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order to analyze microarray data. Two of the most known free analysis software packages are the R-based Bioconductor and dChip. The part of dChip software concerning the calculation and the analysis of gene expression has been modified to permit its execution on both cluster environments (supercomputers) and Grid infrastructures (distributed computing).This work is not aimed at replacing existing tools, but it provides researchers with a method to analyze large datasets without any hardware or software constraints.ResultsAn application able to perform the computation and the analysis of gene expression on large datasets has been developed using algorithms provided by dChip. Different tests have been carried out in order to validate the results and to compare the performances obtained on different infrastructures. Validation tests have been performed using a small dataset related to the comparison of HUVEC (Human Umbilical Vein Endothelial Cells) and Fibroblasts, derived from same donors, treated with IFN-α.Moreover performance tests have been executed just to compare performances on different environments using a large dataset including about 1000 samples related to Breast Cancer patients.ConclusionA Grid-enabled software application for the analysis of large Microarray datasets has been proposed. DChip software has been ported on Linux platform and modified, using appropriate parallelization strategies, to permit its execution on both cluster environments and Grid infrastructures. The added value provided by the use of Grid technologies is the possibility to exploit both computational and data Grid infrastructures to analyze large datasets of distributed data. The software has been validated and performances on cluster and Grid environments have been compared obtaining quite good scalability results.
Highlights
Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area
An application able to perform the computation and the analysis of gene expression on large datasets has been developed using algorithms provided by dChip
Validation tests have been performed using a small dataset related to the comparison of HUVEC (Human Umbilical Vein Endothelial Cells) and Fibroblasts, derived from same donors, treated with IFN-α
Summary
Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. One of the most promising and reactive fields is certainly the microarray technology, which has had, so far, a great scientific impact and a wide application area. Thanks to the microarray technology a large number of genes may be investigated at the same time to find which are differentially expressed on a certain cell type. Quantitative researchers have proposed a variety of methods for handling probe-level data from Affymetrix® oligonucleotide arrays. Such methods employ different procedures for adjusting background fluorescence, normalizing data, incorporating information from "mismatch" probes, and summarizing probe sets
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