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Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

José Luiz Rybarczyk¹, Mauro A. A. Castro¹, Rodrigo J. S. Dalmolin², José C. F. Moreira², Leonardo G. Brunnet¹ & Rita M. C. de Almeida¹

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1. Universidade Federal do Rio Grande do Sul, Physics Department
2. Universidade Federal do Rio Grande do Sul, Biochemistry Department

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Document Type:

Manuscript

Date:

Received 16 October 2009 15:38 UTC; Posted 19 October 2009

Subjects:

Biotechnology, Genetics & Genomics, Bioinformatics

Tags:

• genome analysis
• transcriptome
• gene network
• Monte Carlo dynamics
• Transcriptogram

Abstract:

A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms.

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Rybarczyk, José Luiz, Castro, Mauro, Dalmolin, Rodrigo, Moreira, José, Brunnet, Leonardo, and de Almeida, Rita. Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3869.1> (2009)

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