Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens

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.; Lim, Z. Z. E.; Guan, J. S.; Tan, I. J. L.; Arong, T. J.; Mutwil, M.

doi:10.1101/2021.08.02.454836

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bioRxiv · 10.1101/2021.08.02.454836

Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens

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Abstract

SummaryThe bacterial kingdom comprises unicellular prokaryotes able to establish symbioses from mutualism to parasitism. To combat bacterial pathogenicity, we need an enhanced understanding of gene function and regulation, which will mediate the development of novel antimicrobials. Gene expression can predict gene function, but there lacks a database enabling expansive inter- and intraspecific exploration of gene expression profiles and co-expression networks for bacteria. To address this, we integrated the genomic and transcriptomic data of the 17 most notorious and studied bacterial pathogens, creating bacteria.guru, an interactive database that can identify, visualize, and compare gene expression profiles, co-expression 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 the discovery of multi-faceted antibiotic targets. Hence, we believe bacteria.guru will facilitate future bacterial research. AvailabilityThe database and co-expression networks are freely available from https://bacteria.guru/. The sample annotations are found in the supplemental data.

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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., Lim, Z. Z. E., Guan, J. S., Tan, I. J. L., Arong, T. J., Mutwil, M.. 2021-08-04. Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens. https://doi.org/10.1101/2021.08.02.454836

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