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Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.doc

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Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein

BMC Bioinformatics BioMedCentral Methodology article Open Access Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein Gajendra PS Raghava*1,2 and Joon H Han1 Address: 1Department of Computer Science and Engineering, Pohang University of Science and Technology, San 31 Hyo-Ja Dong, Pohang 790– 784, Republic of Korea and 2Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarh-160036, India Email: Gajendra PS Raghava* - raghava@imtech.res.in; Joon H Han - joonhan@postech.ac.kr * Corresponding author Published: 17 March 2005 Received: 14 August 2004 Accepted: 17 March 2005 BMC Bioinformatics 2005, 6:59 doi:10.1186/1471-2105-6-59 This article is available from: /1471-2105/6/59 ? 2005 Raghava and Han; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: A large number of papers have been published on analysis of microarray data with particular emphasis on normalization of data, detection of differentially expressed genes, clustering of genes and regulatory network. On other hand there are only few studies on relation between expression level and composition of nucleotide/protein sequence, using expression data. There is a need to understand why particular genes/proteins express more in particular conditions. In this study, we analyze 3468 genes of Saccharomyces cerevisiae obtained from Holstege et al., (1998) to understand the relationship between expression level and amino acid composition. Results: We compute the correlation between expression of a gene and amino acid composition of its protein. It was observed that some residues (like Ala, Gly, Arg and Val) have significant positive correlation (r 0.2