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Evaluation of diversity, specialization, and gene specificity in transcriptomes

Octavio Martinez¹ and Humberto Reyes-Valdés²

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1. Laboratorio Nacional de Genómica para la Biodiversidad (Langebio) Cinvestav Irapuato, México.
2. Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, México

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Document Type:

Poster

Date:

Received 31 March 2009 19:17 UTC; Posted 02 April 2009

Subjects:

Genetics & Genomics, Bioinformatics

Tags:

• SAGE
• microarray
• transcriptome
• specialization
• diversity
• high throughput sequencing
• gene specificity

Abstract:

The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. Recently we proposed an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. This approach can be useful for the determination and measure of transcriptional networks. We defined transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. This enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli. We present statistical tools based on resampling procedures to obtain confidence intervals for the parameters as well as perform statistical test. These approaches are illustrated with a human dataset.

Presented at:

4th EMBO Conference: From Functional Genomics to Systems Biology, 15 November 2008

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

How to cite this document:

Martinez, Octavio and Reyes-Valdés, Humberto. Evaluation of diversity, specialization, and gene specificity in transcriptomes. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3012.1> (2009)

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