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Entropy 2019, 21(2), 195; https://doi.org/10.3390/e21020195

Spatial Organization of the Gene Regulatory Program: An Information Theoretical Approach to Breast Cancer Transcriptomics

1
Computational Genomics Division, National Institute of Genomic Medicine, Tlalpan 14610, Ciudad de México, Mexico
2
Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacan 04510, Ciudad de México, Mexico
*
Author to whom correspondence should be addressed.
Received: 21 December 2018 / Revised: 29 January 2019 / Accepted: 1 February 2019 / Published: 19 February 2019
(This article belongs to the Special Issue Information Theory in Complex Systems)
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Abstract

Gene regulation may be studied from an information-theoretic perspective. Gene regulatory programs are representations of the complete regulatory phenomenon associated to each biological state. In diseases such as cancer, these programs exhibit major alterations, which have been associated with the spatial organization of the genome into chromosomes. In this work, we analyze intrachromosomal, or cis-, and interchromosomal, or trans-gene regulatory programs in order to assess the differences that arise in the context of breast cancer. We find that using information theoretic approaches, it is possible to differentiate cis-and trans-regulatory programs in terms of the changes that they exhibit in the breast cancer context, indicating that in breast cancer there is a loss of trans-regulation. Finally, we use these programs to reconstruct a possible spatial relationship between chromosomes. View Full-Text
Keywords: gene regulatory program; mutual information; markov random field; spatial dependency structures; cancer transcriptomics gene regulatory program; mutual information; markov random field; spatial dependency structures; cancer transcriptomics
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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de Anda-Jáuregui, G.; Espinal-Enriquez, J.; Hernández-Lemus, E. Spatial Organization of the Gene Regulatory Program: An Information Theoretical Approach to Breast Cancer Transcriptomics. Entropy 2019, 21, 195.

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