Construction Of Platform For Analyzing And Mining DNA Microarray Data Based On R Language

DNA microarray (i.e, gene chips), a great technology developed in the end of thelast century is by far one of the most important techniques for gene expression andregulation research. As DNA microarray data grow in the public repository, it is thebiggest challenge for biologists to extract and discover the useful biological knowledgefrom the vast amounts of data. At present, there are various softwares for microarraydata analysis, but most modularized softwares are not suitable for secondarydevelopment, analysis modular, or introduced into the new algorithms.For in-depth analysis and mining important information embedded in the DNAmicroarray data, a local platform for microarray data analysis and mining had been builtbased on R language, free Bioconductor project and other software packages in thisstudy, firstly. Then, prementioned data analysis plotforn has been tested via GSE470,the raw data of Affymetrix oligonucleotide microarray published in the open database.Finally, we performed a series of operational testing, such as data obtaining,preprocessing, normalization, quality control, screening of the differentially expressedgenes, gene ontology annotation, clustering analysis, pathway analysis, construction ofgene regulation network, analysis for molecular interaction network, and so on.The above test results using the GSE470microarray data showed that there were33genes differentially expressed between asthmatic patients with normal human,including PIP, MMP1, PDPN, and so on. And the oxidative phosphorylation pathwayhas been significantly changed between asthma and normal groups. Meanwhile, a generegulation and interaction network associated with asthma was found on our platform,and in this network, MMP1, S100a7, DBC1and RPA2are key nodes involved incross-talking in cell signal transmission and molecular interaction. These predictingoutcomes are in accord with several published literature and paper.In addition, comprehensive analysis and judgement for three data sets (GSE470,GSE13396and GSE41649) using the analytical platform built on local PC showedmultiple pathways haed undergone significant changes in asthmatic human, suggestingthat these signaling pathways may provide some evidences for the molecularmechanism of asthma pathology.By system testing for our platform via GSE470microarray data, the results alsoshowed that the system built on local windows platform for microarray data analysis can be quickly and efficiently used for processing and analyzing gene chip such asAffymetrix oligonucleotide microarray data, and extract many useful knowledgesunderlying the a large number of bioinformatics data. So, this study will help theresearchers to understand the molecular mechanisms of disease and biological problem,and promote the development of life sciences and medicine.