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Grid Methodology for Identifying Co-Regulated Genes and Transcription Factor Binding Sites

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6 Author(s)

The identification of the genes that are coordinately regulated is an important and challenging task of bioinformatics and represents a first step in the elucidation of the topology of transcriptional networks. We first compare the performances, in a grid setting, of the Markov clustering algorithm with respect to the k-means using microarray test data sets. The gene expression information of the clustered genes can be used to annotate transcription binding sites upstream co-regulated genes. The methodology uses a regression model that relates gene expression levels to the matching scores of nucleotide patterns allowing us to identify DNA-binding sites from a collection of noncoding DNA sequences from co-regulated genes. Here we discuss extending the approach to multiple species exploiting the grid framework.

Published in:

IEEE Transactions on NanoBioscience  (Volume:6 ,  Issue: 2 )