Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha
The plant kingdom is home to a diverse collection of secondary metabolites with tremendous economic and therapeutic value. Secondary metabolite pathways are difficult to fully uncover for various reasons. Co-expression network analysis offers bioinformatic techniques and insights into fully elucidat...
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| Format: | Final Year Project (FYP) |
| Language: | English |
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Nanyang Technological University
2022
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| Online Access: | https://hdl.handle.net/10356/157765 |
| _version_ | 1826122175989415936 |
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| author | Lee, Adrian Ming Jern |
| author2 | Marek Mutwil |
| author_facet | Marek Mutwil Lee, Adrian Ming Jern |
| author_sort | Lee, Adrian Ming Jern |
| collection | NTU |
| description | The plant kingdom is home to a diverse collection of secondary metabolites with tremendous economic and therapeutic value. Secondary metabolite pathways are difficult to fully uncover for various reasons. Co-expression network analysis offers bioinformatic techniques and insights into fully elucidating these networks. The basal land plant Marchantia polymorpha’s genome containing limited genetic redundancy offers an exciting genetic window into the evolution of terrestrial land plants. In this project, co-expression networks of M. polymorpha were analysed to identify biological pathways, of which 85 pathways were found. While it is possible to identify biological pathways with this analysis, the predictive quality of the network still has room for improvement. Integration of enzyme commission numbers to the network, as a novel centrality-like edge weight, to identify true relationships was shown to improve network quality scores by up to 1.3 times. However, the predictive ability of the final network is still far from optimal, which highlights the need to address other possible limitations in the network, one possibility is the composition-bias of RNA-sequencing experiments. |
| first_indexed | 2024-10-01T05:44:12Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/157765 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:44:12Z |
| publishDate | 2022 |
| publisher | Nanyang Technological University |
| record_format | dspace |
| spelling | ntu-10356/1577652023-02-28T18:09:21Z Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha Lee, Adrian Ming Jern Marek Mutwil School of Biological Sciences mutwil@ntu.edu.sg Science::Biological sciences::Genetics The plant kingdom is home to a diverse collection of secondary metabolites with tremendous economic and therapeutic value. Secondary metabolite pathways are difficult to fully uncover for various reasons. Co-expression network analysis offers bioinformatic techniques and insights into fully elucidating these networks. The basal land plant Marchantia polymorpha’s genome containing limited genetic redundancy offers an exciting genetic window into the evolution of terrestrial land plants. In this project, co-expression networks of M. polymorpha were analysed to identify biological pathways, of which 85 pathways were found. While it is possible to identify biological pathways with this analysis, the predictive quality of the network still has room for improvement. Integration of enzyme commission numbers to the network, as a novel centrality-like edge weight, to identify true relationships was shown to improve network quality scores by up to 1.3 times. However, the predictive ability of the final network is still far from optimal, which highlights the need to address other possible limitations in the network, one possibility is the composition-bias of RNA-sequencing experiments. Bachelor of Science in Biological Sciences 2022-05-23T04:34:01Z 2022-05-23T04:34:01Z 2022 Final Year Project (FYP) Lee, A. M. J. (2022). Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/157765 https://hdl.handle.net/10356/157765 en application/pdf Nanyang Technological University |
| spellingShingle | Science::Biological sciences::Genetics Lee, Adrian Ming Jern Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title | Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title_full | Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title_fullStr | Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title_full_unstemmed | Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title_short | Co-expression network analysis for identification of secondary metabolite pathways in Marchantia polymorpha |
| title_sort | co expression network analysis for identification of secondary metabolite pathways in marchantia polymorpha |
| topic | Science::Biological sciences::Genetics |
| url | https://hdl.handle.net/10356/157765 |
| work_keys_str_mv | AT leeadrianmingjern coexpressionnetworkanalysisforidentificationofsecondarymetabolitepathwaysinmarchantiapolymorpha |