Exploiting plant transcriptomic databases: resources, tools, and approaches
There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by...
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sg-ntu-dr.10356-1610362023-02-28T17:13:22Z Exploiting plant transcriptomic databases: resources, tools, and approaches Lim, Peng Ken Zheng, Xinghai Goh, Jong Ching Mutwil, Marek School of Biological Sciences Science::Biological sciences Gene Expression Comparative Transcriptomics There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools. Ministry of Education (MOE) Singapore Food Agency Published version This review was supported by a Singapore Ministry of Education tier-two grant (MOE2018-T2-2-053) and a Singapore Food Agency grant (SFS_RND_SUFP_001_05). 2022-08-12T05:04:30Z 2022-08-12T05:04:30Z 2022 Journal Article Lim, P. K., Zheng, X., Goh, J. C. & Mutwil, M. (2022). Exploiting plant transcriptomic databases: resources, tools, and approaches. Plant Communications, 3(4), 100323-. https://dx.doi.org/10.1016/j.xplc.2022.100323 2590-3462 https://hdl.handle.net/10356/161036 10.1016/j.xplc.2022.100323 35605200 2-s2.0-85129566821 4 3 100323 en MOE2018-T2-2-053 SFS-RND-SUFP-001-05 Plant Communications © 2022 The Author(s). Published by the Plant Communications Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and CEMPS, CAS. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). application/pdf |
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Science::Biological sciences Gene Expression Comparative Transcriptomics Lim, Peng Ken Zheng, Xinghai Goh, Jong Ching Mutwil, Marek Exploiting plant transcriptomic databases: resources, tools, and approaches |
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There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools. |
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School of Biological Sciences |
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School of Biological Sciences Lim, Peng Ken Zheng, Xinghai Goh, Jong Ching Mutwil, Marek |
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Article |
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Lim, Peng Ken Zheng, Xinghai Goh, Jong Ching Mutwil, Marek |
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Lim, Peng Ken |
title |
Exploiting plant transcriptomic databases: resources, tools, and approaches |
title_short |
Exploiting plant transcriptomic databases: resources, tools, and approaches |
title_full |
Exploiting plant transcriptomic databases: resources, tools, and approaches |
title_fullStr |
Exploiting plant transcriptomic databases: resources, tools, and approaches |
title_full_unstemmed |
Exploiting plant transcriptomic databases: resources, tools, and approaches |
title_sort |
exploiting plant transcriptomic databases: resources, tools, and approaches |
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2022 |
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https://hdl.handle.net/10356/161036 |
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1759856755228016640 |