Kingdom-wide resource for gene expression in plants
Diverse plant groups can benefit humanity in various ways. To date, there is untapped knowledge in 380000 publicly-available plant RNA-seq samples. Currently, several databases repurpose large numbers of RNA-seq samples for several species, allowing biologists to gain insights from these data. Howev...
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2022
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sg-ntu-dr.10356-1629542023-02-28T18:08:50Z Kingdom-wide resource for gene expression in plants Goh, William Marek Mutwil School of Biological Sciences mutwil@ntu.edu.sg Science::Biological sciences Diverse plant groups can benefit humanity in various ways. To date, there is untapped knowledge in 380000 publicly-available plant RNA-seq samples. Currently, several databases repurpose large numbers of RNA-seq samples for several species, allowing biologists to gain insights from these data. However, many species are still not represented in the existing databases despite the availability of data. We have previously developed the software capability to process all the plant RNA-seq data in less than a month and obtained organ annotations. These pave the way for this project, which sets out to develop a web application (Plant Gene Expression Omnibus) to make gene expression insights for 103 species accessible to biologists. Currently, we address how a gene is expressed across organs, its organ specificity, and also identify all specifically-expressed genes for each organ. The design is scalable to include more species and more advanced features, and we discuss the next steps for development, to contribute towards realizing kingdom-wide gene expression analysis. Bachelor of Science in Biological Sciences 2022-11-14T07:43:12Z 2022-11-14T07:43:12Z 2022 Final Year Project (FYP) Goh, W. (2022). Kingdom-wide resource for gene expression in plants. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/162954 https://hdl.handle.net/10356/162954 en application/pdf Nanyang Technological University |
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Science::Biological sciences Goh, William Kingdom-wide resource for gene expression in plants |
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Diverse plant groups can benefit humanity in various ways. To date, there is untapped knowledge in 380000 publicly-available plant RNA-seq samples. Currently, several databases repurpose large numbers of RNA-seq samples for several species, allowing biologists to gain insights from these data. However, many species are still not represented in the existing databases despite the availability of data. We have previously developed the software capability to process all the plant RNA-seq data in less than a month and obtained organ annotations. These pave the way for this project, which sets out to develop a web application (Plant Gene Expression Omnibus) to make gene expression insights for 103 species accessible to biologists. Currently, we address how a gene is expressed across organs, its organ specificity, and also identify all specifically-expressed genes for each organ. The design is scalable to include more species and more advanced features, and we discuss the next steps for development, to contribute towards realizing kingdom-wide gene expression analysis. |
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Marek Mutwil |
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Marek Mutwil Goh, William |
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Final Year Project |
author |
Goh, William |
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Goh, William |
title |
Kingdom-wide resource for gene expression in plants |
title_short |
Kingdom-wide resource for gene expression in plants |
title_full |
Kingdom-wide resource for gene expression in plants |
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Kingdom-wide resource for gene expression in plants |
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Kingdom-wide resource for gene expression in plants |
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kingdom-wide resource for gene expression in plants |
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Nanyang Technological University |
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2022 |
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https://hdl.handle.net/10356/162954 |
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