Nascimben Mauro, Rimondini Lia
Department of Health Sciences, Università del Piemonte Orientale UPO, Corso Trieste 15/A, 28100, Novara, Italy.
Curr Microbiol. 2025 Sep 9;82(10):497. doi: 10.1007/s00284-025-04435-3.
A Python-scripted software tool has been developed to help study the heterogeneity of gene changes, markedly or moderately expressed, when several experimental conditions are compared. The analysis workflow encloses a scorecard that groups genes based on relative fold-change and statistical significance, providing additional functions that facilitate knowledge extraction. The scorecard reports highlight unique patterns of gene regulation, such as genes whose expression is consistently up- or down-regulated across experiments, all of which are supported by graphs and summaries to characterize the dataset under investigation. Four GEO datasets related to RNA-seq bacterial biofilm expression levels were independently analyzed for information mining through the functionalities of the software library. The scorecard identified and tracked, over time or experiments, genes meaningful for bacterial metabolism and survival in response to antibiotics, adjuvants, and biocompatible materials. Analyses detected factors and strategies to persist in the environment by bacterial aggregates, such as modifications in the binding affinity of penicillin-related proteins or ribosomal subunits, the development of alternative metabolic pathways, cell wall thickening, intracellular concentration of drugs reduced by efflux pumps, and enzymatic inactivation through hydrolyzation, phosphorylation, or adenylation.
已经开发了一种用Python编写的软件工具，以帮助研究在比较几种实验条件时显著或中等表达的基因变化的异质性。分析工作流程包含一个记分卡，该记分卡根据相对倍数变化和统计显著性对基因进行分组，并提供有助于知识提取的附加功能。记分卡报告突出了独特的基因调控模式，例如在各个实验中表达持续上调或下调的基因，所有这些都由图表和总结来支持，以表征所研究的数据集。通过软件库的功能，对四个与RNA测序细菌生物膜表达水平相关的GEO数据集进行了独立分析，以挖掘信息。记分卡随着时间或实验的推移，识别并追踪了对细菌在抗生素、佐剂和生物相容性材料作用下的代谢和存活有意义的基因。分析检测到细菌聚集体在环境中持续存在的因素和策略，例如青霉素相关蛋白或核糖体亚基结合亲和力的改变、替代代谢途径的发展、细胞壁增厚、外排泵降低药物的细胞内浓度以及通过水解、磷酸化或腺苷化进行的酶失活。
