Optimized probe masking for comparative transcriptomics of closely related species.

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as co...

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Autores principales:	Yvonne Poeschl, Carolin Delker, Jana Trenner, Kristian Karsten Ullrich, Marcel Quint, Ivo Grosse
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a721cde95b6e4925a343f4e73a07054e
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spelling	oai:doaj.org-article:a721cde95b6e4925a343f4e73a07054e2021-11-18T08:47:40ZOptimized probe masking for comparative transcriptomics of closely related species.1932-620310.1371/journal.pone.0078497https://doaj.org/article/a721cde95b6e4925a343f4e73a07054e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24260119/?tool=EBIhttps://doaj.org/toc/1932-6203Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses.Yvonne PoeschlCarolin DelkerJana TrennerKristian Karsten UllrichMarcel QuintIvo GrossePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e78497 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yvonne Poeschl Carolin Delker Jana Trenner Kristian Karsten Ullrich Marcel Quint Ivo Grosse Optimized probe masking for comparative transcriptomics of closely related species.
description	Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses.
format	article
author	Yvonne Poeschl Carolin Delker Jana Trenner Kristian Karsten Ullrich Marcel Quint Ivo Grosse
author_facet	Yvonne Poeschl Carolin Delker Jana Trenner Kristian Karsten Ullrich Marcel Quint Ivo Grosse
author_sort	Yvonne Poeschl
title	Optimized probe masking for comparative transcriptomics of closely related species.
title_short	Optimized probe masking for comparative transcriptomics of closely related species.
title_full	Optimized probe masking for comparative transcriptomics of closely related species.
title_fullStr	Optimized probe masking for comparative transcriptomics of closely related species.
title_full_unstemmed	Optimized probe masking for comparative transcriptomics of closely related species.
title_sort	optimized probe masking for comparative transcriptomics of closely related species.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/a721cde95b6e4925a343f4e73a07054e
work_keys_str_mv	AT yvonnepoeschl optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies AT carolindelker optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies AT janatrenner optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies AT kristiankarstenullrich optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies AT marcelquint optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies AT ivogrosse optimizedprobemaskingforcomparativetranscriptomicsofcloselyrelatedspecies
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Optimized probe masking for comparative transcriptomics of closely related species.

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