A method for identification of putatively co-regulated genes

by Andersson, Malin

Abstract (Summary)
The genomes of several organisms have been sequenced and the need for methods to analyse the data is growing. In this project a method is described that tries to identify co-regulated genes. The method identifies transcription factor binding sites, documented in TRANSFAC, in the non-coding regions of genes. The algorithm counts the number of common binding sites and the number of unique binding sites for each pair of genes and decides if the genes are co-regulated. The result of the method is compared with the correlation between the gene expression patterns of the genes. The method is tested on 21 gene pairs from the genome of Saccharomyces cerevisiae. The algorithm first identified binding sites from all organisms. The accuracy of the program was very low in this case. When the algorithm was modified to only identify binding sites found in plants the accuracy was much improved, from 52% to 76% correct predictions.
Bibliographical Information:


School:Högskolan i Skövde

School Location:Sweden

Source Type:Master's Thesis

Keywords:co regulated genes binding site transfac gene expression


Date of Publication:02/04/2008

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