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Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product, which may be proteins. A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is sta...

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Autores principales: Anjum, Arfa, Jaggi, Seema, Varghese, Eldho, Lall, Shwetank, Bhowmik, Arpan, Rai, Anil
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Mary Ann Liebert, Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827276/
https://www.ncbi.nlm.nih.gov/pubmed/26949988
http://dx.doi.org/10.1089/cmb.2015.0205
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author Anjum, Arfa
Jaggi, Seema
Varghese, Eldho
Lall, Shwetank
Bhowmik, Arpan
Rai, Anil
author_facet Anjum, Arfa
Jaggi, Seema
Varghese, Eldho
Lall, Shwetank
Bhowmik, Arpan
Rai, Anil
author_sort Anjum, Arfa
collection PubMed
description Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product, which may be proteins. A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is statistically significant. To identify differentially expressed genes between two conditions, it is important to find statistical distributional property of the data to approximate the nature of differential genes. In the present study, the focus is mainly to investigate the differential gene expression analysis for sequence data based on compound distribution model. This approach was applied in RNA-seq count data of Arabidopsis thaliana and it has been found that compound Poisson distribution is more appropriate to capture the variability as compared with Poisson distribution. Thus, fitting of appropriate distribution to gene expression data provides statistically sound cutoff values for identifying differentially expressed genes.
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spelling pubmed-48272762016-04-20 Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach Anjum, Arfa Jaggi, Seema Varghese, Eldho Lall, Shwetank Bhowmik, Arpan Rai, Anil J Comput Biol Research Articles Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product, which may be proteins. A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is statistically significant. To identify differentially expressed genes between two conditions, it is important to find statistical distributional property of the data to approximate the nature of differential genes. In the present study, the focus is mainly to investigate the differential gene expression analysis for sequence data based on compound distribution model. This approach was applied in RNA-seq count data of Arabidopsis thaliana and it has been found that compound Poisson distribution is more appropriate to capture the variability as compared with Poisson distribution. Thus, fitting of appropriate distribution to gene expression data provides statistically sound cutoff values for identifying differentially expressed genes. Mary Ann Liebert, Inc. 2016-04-01 /pmc/articles/PMC4827276/ /pubmed/26949988 http://dx.doi.org/10.1089/cmb.2015.0205 Text en © Arfa Anjum et al., 2016. Published by Mary Ann Liebert, Inc. This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the orginal author(s) and the source are credited.
spellingShingle Research Articles
Anjum, Arfa
Jaggi, Seema
Varghese, Eldho
Lall, Shwetank
Bhowmik, Arpan
Rai, Anil
Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title_full Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title_fullStr Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title_full_unstemmed Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title_short Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach
title_sort identification of differentially expressed genes in rna-seq data of arabidopsis thaliana: a compound distribution approach
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827276/
https://www.ncbi.nlm.nih.gov/pubmed/26949988
http://dx.doi.org/10.1089/cmb.2015.0205
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