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Longitudinal Analysis of Contrasts in Gene Expression Data

We are interested in detecting a departure from the baseline in a longitudinal analysis in the context of multiple organ dysfunction syndrome (MODS). In particular, we are given gene expression reads at two time points for a fixed number of genes and individuals. The individuals can be subdivided in...

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Autores principales: Hahn, Georg, Novak, Tanya, Crawford, Jeremy C., Randolph, Adrienne G., Lange, Christoph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10298400/
https://www.ncbi.nlm.nih.gov/pubmed/37372314
http://dx.doi.org/10.3390/genes14061134
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author Hahn, Georg
Novak, Tanya
Crawford, Jeremy C.
Randolph, Adrienne G.
Lange, Christoph
author_facet Hahn, Georg
Novak, Tanya
Crawford, Jeremy C.
Randolph, Adrienne G.
Lange, Christoph
author_sort Hahn, Georg
collection PubMed
description We are interested in detecting a departure from the baseline in a longitudinal analysis in the context of multiple organ dysfunction syndrome (MODS). In particular, we are given gene expression reads at two time points for a fixed number of genes and individuals. The individuals can be subdivided into two groups, denoted as groups A and B. Using the two time points, we compute a contrast of gene expression reads per individual and gene. The age of each individual is known and it is used to compute, for each gene separately, a linear regression of the gene expression contrasts on the individual’s age. Looking at the intercept of the linear regression to detect a departure from the baseline, we aim to reliably single out those genes for which there is a difference in the intercept among those individuals in group A and not in group B. In this work, we develop testing methodology for this setting based on two hypothesis tests—one under the null and one under an appropriately formulated alternative. We demonstrate the validity of our approach using a dataset created by bootstrapping from a real data application in the context of multiple organ dysfunction syndrome (MODS).
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spelling pubmed-102984002023-06-28 Longitudinal Analysis of Contrasts in Gene Expression Data Hahn, Georg Novak, Tanya Crawford, Jeremy C. Randolph, Adrienne G. Lange, Christoph Genes (Basel) Article We are interested in detecting a departure from the baseline in a longitudinal analysis in the context of multiple organ dysfunction syndrome (MODS). In particular, we are given gene expression reads at two time points for a fixed number of genes and individuals. The individuals can be subdivided into two groups, denoted as groups A and B. Using the two time points, we compute a contrast of gene expression reads per individual and gene. The age of each individual is known and it is used to compute, for each gene separately, a linear regression of the gene expression contrasts on the individual’s age. Looking at the intercept of the linear regression to detect a departure from the baseline, we aim to reliably single out those genes for which there is a difference in the intercept among those individuals in group A and not in group B. In this work, we develop testing methodology for this setting based on two hypothesis tests—one under the null and one under an appropriately formulated alternative. We demonstrate the validity of our approach using a dataset created by bootstrapping from a real data application in the context of multiple organ dysfunction syndrome (MODS). MDPI 2023-05-24 /pmc/articles/PMC10298400/ /pubmed/37372314 http://dx.doi.org/10.3390/genes14061134 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hahn, Georg
Novak, Tanya
Crawford, Jeremy C.
Randolph, Adrienne G.
Lange, Christoph
Longitudinal Analysis of Contrasts in Gene Expression Data
title Longitudinal Analysis of Contrasts in Gene Expression Data
title_full Longitudinal Analysis of Contrasts in Gene Expression Data
title_fullStr Longitudinal Analysis of Contrasts in Gene Expression Data
title_full_unstemmed Longitudinal Analysis of Contrasts in Gene Expression Data
title_short Longitudinal Analysis of Contrasts in Gene Expression Data
title_sort longitudinal analysis of contrasts in gene expression data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10298400/
https://www.ncbi.nlm.nih.gov/pubmed/37372314
http://dx.doi.org/10.3390/genes14061134
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