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A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome

The overrepresented approach (ORA) is the most widely-accepted method for functional analysis of microarray datasets. The ORA is computationally-efficient and robust; however, it suffers from the inability of comparing results from multiple gene lists particularly with time-course experiments or tho...

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Autores principales: Bionaz, Massimo, Periasamy, Kathiravan, Rodriguez-Zas, Sandra L., Hurley, Walter L., Loor, Juan J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306320/
https://www.ncbi.nlm.nih.gov/pubmed/22438877
http://dx.doi.org/10.1371/journal.pone.0032455
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author Bionaz, Massimo
Periasamy, Kathiravan
Rodriguez-Zas, Sandra L.
Hurley, Walter L.
Loor, Juan J.
author_facet Bionaz, Massimo
Periasamy, Kathiravan
Rodriguez-Zas, Sandra L.
Hurley, Walter L.
Loor, Juan J.
author_sort Bionaz, Massimo
collection PubMed
description The overrepresented approach (ORA) is the most widely-accepted method for functional analysis of microarray datasets. The ORA is computationally-efficient and robust; however, it suffers from the inability of comparing results from multiple gene lists particularly with time-course experiments or those involving multiple treatments. To overcome such limitation a novel method termed Dynamic Impact Approach (DIA) is proposed. The DIA provides an estimate of the biological impact of the experimental conditions and the direction of the impact. The impact is obtained by combining the proportion of differentially expressed genes (DEG) with the log2 mean fold change and mean –log P-value of genes associated with the biological term. The direction of the impact is calculated as the difference of the impact of up-regulated DEG and down-regulated DEG associated with the biological term. The DIA was validated using microarray data from a time-course experiment of bovine mammary gland across the lactation cycle. Several annotation databases were analyzed with DIA and compared to the same analysis performed by the ORA. The DIA highlighted that during lactation both BTA6 and BTA14 were the most impacted chromosomes; among Uniprot tissues those related with lactating mammary gland were the most positively-impacted; within KEGG pathways ‘Galactose metabolism’ and several metabolism categories related to lipid synthesis were among the most impacted and induced; within Gene Ontology “lactose biosynthesis” among Biological processes and “Lactose synthase activity” and “Stearoyl-CoA 9-desaturase activity” among Molecular processes were the most impacted and induced. With the exception of the terms ‘Milk’, ‘Milk protein’ and ‘Mammary gland’ among Uniprot tissues and SP_PIR_Keyword, the use of ORA failed to capture as significantly-enriched (i.e., biologically relevant) any term known to be associated with lactating mammary gland. Results indicate the DIA is a biologically-sound approach for analysis of time-course experiments. This tool represents an alternative to ORA for functional analysis.
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spelling pubmed-33063202012-03-21 A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome Bionaz, Massimo Periasamy, Kathiravan Rodriguez-Zas, Sandra L. Hurley, Walter L. Loor, Juan J. PLoS One Research Article The overrepresented approach (ORA) is the most widely-accepted method for functional analysis of microarray datasets. The ORA is computationally-efficient and robust; however, it suffers from the inability of comparing results from multiple gene lists particularly with time-course experiments or those involving multiple treatments. To overcome such limitation a novel method termed Dynamic Impact Approach (DIA) is proposed. The DIA provides an estimate of the biological impact of the experimental conditions and the direction of the impact. The impact is obtained by combining the proportion of differentially expressed genes (DEG) with the log2 mean fold change and mean –log P-value of genes associated with the biological term. The direction of the impact is calculated as the difference of the impact of up-regulated DEG and down-regulated DEG associated with the biological term. The DIA was validated using microarray data from a time-course experiment of bovine mammary gland across the lactation cycle. Several annotation databases were analyzed with DIA and compared to the same analysis performed by the ORA. The DIA highlighted that during lactation both BTA6 and BTA14 were the most impacted chromosomes; among Uniprot tissues those related with lactating mammary gland were the most positively-impacted; within KEGG pathways ‘Galactose metabolism’ and several metabolism categories related to lipid synthesis were among the most impacted and induced; within Gene Ontology “lactose biosynthesis” among Biological processes and “Lactose synthase activity” and “Stearoyl-CoA 9-desaturase activity” among Molecular processes were the most impacted and induced. With the exception of the terms ‘Milk’, ‘Milk protein’ and ‘Mammary gland’ among Uniprot tissues and SP_PIR_Keyword, the use of ORA failed to capture as significantly-enriched (i.e., biologically relevant) any term known to be associated with lactating mammary gland. Results indicate the DIA is a biologically-sound approach for analysis of time-course experiments. This tool represents an alternative to ORA for functional analysis. Public Library of Science 2012-03-16 /pmc/articles/PMC3306320/ /pubmed/22438877 http://dx.doi.org/10.1371/journal.pone.0032455 Text en Bionaz et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Bionaz, Massimo
Periasamy, Kathiravan
Rodriguez-Zas, Sandra L.
Hurley, Walter L.
Loor, Juan J.
A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title_full A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title_fullStr A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title_full_unstemmed A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title_short A Novel Dynamic Impact Approach (DIA) for Functional Analysis of Time-Course Omics Studies: Validation Using the Bovine Mammary Transcriptome
title_sort novel dynamic impact approach (dia) for functional analysis of time-course omics studies: validation using the bovine mammary transcriptome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306320/
https://www.ncbi.nlm.nih.gov/pubmed/22438877
http://dx.doi.org/10.1371/journal.pone.0032455
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