Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens
While bacteria can be beneficial to our health, their deadly pathogenic potential has been an ever-present concern exacerbated by the emergence of drug-resistant strains. As such, there is a pressing urgency for an enhanced understanding of their gene function and regulation, which could mediate the...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/161692 |
| _version_ | 1826120930733064192 |
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| author | Lim, Peng Ken Davey, Emilia Emmanuelle Wee, Sean Seetoh, Wei Song Goh, Jong Ching Zheng, Xinghai Phang, Sean Kia Ann Seah, Eugene Sheng Kai Ng, Janice Wan Zhen Wee, Xavier Jia Hui Quek, Aloysius Jun Hui Lim, Jordan JingHeng Rodrigues, Edbert Edric Lee, Heesoo Lim, Chin Yong Tan, Wei Zhi Dan, Yuet Ruh Lee, Bronson Chee, Samuel En Le Lim, Zachary Ze En Guan, Jia Sheng Tan, Ivan Jia Le Arong, Trinidad Jeremiah Mutwil, Marek |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Lim, Peng Ken Davey, Emilia Emmanuelle Wee, Sean Seetoh, Wei Song Goh, Jong Ching Zheng, Xinghai Phang, Sean Kia Ann Seah, Eugene Sheng Kai Ng, Janice Wan Zhen Wee, Xavier Jia Hui Quek, Aloysius Jun Hui Lim, Jordan JingHeng Rodrigues, Edbert Edric Lee, Heesoo Lim, Chin Yong Tan, Wei Zhi Dan, Yuet Ruh Lee, Bronson Chee, Samuel En Le Lim, Zachary Ze En Guan, Jia Sheng Tan, Ivan Jia Le Arong, Trinidad Jeremiah Mutwil, Marek |
| author_sort | Lim, Peng Ken |
| collection | NTU |
| description | While bacteria can be beneficial to our health, their deadly pathogenic potential has been an ever-present concern exacerbated by the emergence of drug-resistant strains. As such, there is a pressing urgency for an enhanced understanding of their gene function and regulation, which could mediate the development of novel antimicrobials. Transcriptomic analyses have been established as insightful and indispensable to the functional characterization of genes and identification of new biological pathways, but in the context of bacterial studies, they remain limited to species-specific datasets. To address this, we integrated the genomic and transcriptomic data of the 17 most notorious and researched bacterial pathogens, creating bacteria.guru, an interactive database that can identify, visualize, and compare gene expression profiles, coexpression networks, functionally enriched clusters, and gene families across species. Through illustrating antibiotic resistance mechanisms in P. aeruginosa, we demonstrate that bacteria.guru could potentially aid in discovering multi-faceted antibiotic targets and, overall, facilitate future bacterial research. AVAILABILITY: The database and coexpression networks are freely available from https://bacteria.guru/. Sample annotations can be found in the supplemental data. |
| first_indexed | 2024-10-01T05:24:29Z |
| format | Journal Article |
| id | ntu-10356/161692 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:24:29Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1616922023-02-28T17:13:01Z Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens Lim, Peng Ken Davey, Emilia Emmanuelle Wee, Sean Seetoh, Wei Song Goh, Jong Ching Zheng, Xinghai Phang, Sean Kia Ann Seah, Eugene Sheng Kai Ng, Janice Wan Zhen Wee, Xavier Jia Hui Quek, Aloysius Jun Hui Lim, Jordan JingHeng Rodrigues, Edbert Edric Lee, Heesoo Lim, Chin Yong Tan, Wei Zhi Dan, Yuet Ruh Lee, Bronson Chee, Samuel En Le Lim, Zachary Ze En Guan, Jia Sheng Tan, Ivan Jia Le Arong, Trinidad Jeremiah Mutwil, Marek School of Biological Sciences Science::Biological sciences Pathogens Networks While bacteria can be beneficial to our health, their deadly pathogenic potential has been an ever-present concern exacerbated by the emergence of drug-resistant strains. As such, there is a pressing urgency for an enhanced understanding of their gene function and regulation, which could mediate the development of novel antimicrobials. Transcriptomic analyses have been established as insightful and indispensable to the functional characterization of genes and identification of new biological pathways, but in the context of bacterial studies, they remain limited to species-specific datasets. To address this, we integrated the genomic and transcriptomic data of the 17 most notorious and researched bacterial pathogens, creating bacteria.guru, an interactive database that can identify, visualize, and compare gene expression profiles, coexpression networks, functionally enriched clusters, and gene families across species. Through illustrating antibiotic resistance mechanisms in P. aeruginosa, we demonstrate that bacteria.guru could potentially aid in discovering multi-faceted antibiotic targets and, overall, facilitate future bacterial research. AVAILABILITY: The database and coexpression networks are freely available from https://bacteria.guru/. Sample annotations can be found in the supplemental data. Submitted/Accepted version 2022-09-15T05:48:02Z 2022-09-15T05:48:02Z 2022 Journal Article Lim, P. K., Davey, E. E., Wee, S., Seetoh, W. S., Goh, J. C., Zheng, X., Phang, S. K. A., Seah, E. S. K., Ng, J. W. Z., Wee, X. J. H., Quek, A. J. H., Lim, J. J., Rodrigues, E. E., Lee, H., Lim, C. Y., Tan, W. Z., Dan, Y. R., Lee, B., Chee, S. E. L., ...Mutwil, M. (2022). Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens. Journal of Molecular Biology, 434(11), 167380-. https://dx.doi.org/10.1016/j.jmb.2021.167380 0022-2836 https://hdl.handle.net/10356/161692 10.1016/j.jmb.2021.167380 34838806 2-s2.0-85121122226 11 434 167380 en Journal of Molecular Biology © 2021 Elsevier Ltd.. All rights reserved. This paper was published in Journal of Molecular Biology and is made available with permission of Elsevier Ltd. application/pdf |
| spellingShingle | Science::Biological sciences Pathogens Networks Lim, Peng Ken Davey, Emilia Emmanuelle Wee, Sean Seetoh, Wei Song Goh, Jong Ching Zheng, Xinghai Phang, Sean Kia Ann Seah, Eugene Sheng Kai Ng, Janice Wan Zhen Wee, Xavier Jia Hui Quek, Aloysius Jun Hui Lim, Jordan JingHeng Rodrigues, Edbert Edric Lee, Heesoo Lim, Chin Yong Tan, Wei Zhi Dan, Yuet Ruh Lee, Bronson Chee, Samuel En Le Lim, Zachary Ze En Guan, Jia Sheng Tan, Ivan Jia Le Arong, Trinidad Jeremiah Mutwil, Marek Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title | Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title_full | Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title_fullStr | Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title_full_unstemmed | Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title_short | Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens |
| title_sort | bacteria guru comparative transcriptomics and co expression database for bacterial pathogens |
| topic | Science::Biological sciences Pathogens Networks |
| url | https://hdl.handle.net/10356/161692 |
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