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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Main Author: Goh, William
Other Authors: Marek Mutwil
Format: Final Year Project
Language:English
Published: Nanyang Technological University 2022
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Online Access:https://hdl.handle.net/10356/162954
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Institution: Nanyang Technological University
Language: English
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spelling 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
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Science::Biological sciences
spellingShingle Science::Biological sciences
Goh, William
Kingdom-wide resource for gene expression in plants
description 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.
author2 Marek Mutwil
author_facet Marek Mutwil
Goh, William
format Final Year Project
author Goh, William
author_sort 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
title_fullStr Kingdom-wide resource for gene expression in plants
title_full_unstemmed Kingdom-wide resource for gene expression in plants
title_sort kingdom-wide resource for gene expression in plants
publisher Nanyang Technological University
publishDate 2022
url https://hdl.handle.net/10356/162954
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