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 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.

Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.

The fungi kingdom is composed of eukaryotic heterotrophs, which are responsible for balancing the ecosystem and play a major role as decomposers. They also produce a vast diversity of secondary metabolites, which have antibiotic or pharmacological properties. However, our lack of knowledge of gene function in fungi precludes us from tailoring them to our needs and tapping into their metabolic diversity. To help remedy this, we gathered genomic and gene expression data of 19 most widely-researched fungi to build an online tool, fungi.guru, which contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. We exemplify how our tool can elucidate the molecular function, biological process and cellular component of genes involved in various biological processes, by identifying a secondary metabolite pathway producing gliotoxin in Aspergillus fumigatus, the catabolic pathway of cellulose in Coprinopsis cinerea and the conserved DNA replication pathway in Fusarium graminearum and Pyricularia oryzae. The tool is available at www.fungi.guru.