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用于评估病原菌复杂应激反应的 Co-PATHOgenex 网络应用程序。

Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria.

机构信息

Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University , Umeå, Sweden.

Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University , Umeå, Sweden.

出版信息

Microbiol Spectr. 2024 Jan 11;12(1):e0278123. doi: 10.1128/spectrum.02781-23. Epub 2023 Nov 29.

DOI:10.1128/spectrum.02781-23
PMID:38019016
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10783046/
Abstract

Unveiling gene co-expression networks in bacterial pathogens has the potential for gaining insights into their adaptive strategies within the host environment. Here, we developed Co-PATHOgenex, an interactive and user-friendly web application that enables users to construct networks from gene co-expressions using custom-defined thresholds (https://avicanlab.shinyapps.io/copathogenex/). The incorporated search functions and visualizations within the tool simplify the usage and facilitate the interpretation of the analysis output. Co-PATHOgenex also includes stress stimulons for various bacterial species, which can help identify gene products not previously associated with a particular stress condition.

摘要

揭示细菌病原体中的基因共表达网络有助于深入了解它们在宿主环境中的适应策略。在这里，我们开发了 Co-PATHOgenex，这是一个交互式和用户友好的网络应用程序，使用户能够使用自定义定义的阈值从基因共表达构建网络 (https://avicanlab.shinyapps.io/copathogenex/)。该工具中包含的搜索功能和可视化简化了使用过程，并有助于解释分析结果。Co-PATHOgenex 还包含了各种细菌物种的应激启动子，这有助于识别以前与特定应激条件无关的基因产物。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/5a5f68674e77/spectrum.02781-23.f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/c539edcdbf6a/spectrum.02781-23.f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/bf780d2db921/spectrum.02781-23.f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/56a456294ff9/spectrum.02781-23.f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/8e3587b3a211/spectrum.02781-23.f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/a2a5f256d5b8/spectrum.02781-23.f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/5a5f68674e77/spectrum.02781-23.f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/c539edcdbf6a/spectrum.02781-23.f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/bf780d2db921/spectrum.02781-23.f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/56a456294ff9/spectrum.02781-23.f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/8e3587b3a211/spectrum.02781-23.f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/a2a5f256d5b8/spectrum.02781-23.f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7c02/10783046/5a5f68674e77/spectrum.02781-23.f006.jpg

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