Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia.
National-Level Institute for Sustainable Environmental Solutions, Jadranska cesta 28, 2000 Maribor, Slovenia.
Int J Mol Sci. 2024 Sep 23;25(18):10210. doi: 10.3390/ijms251810210.
Curated online interaction databases and gene ontology tools have streamlined the analysis of highly complex gene/protein networks. However, understanding of disease pathogenesis has gradually shifted from a protein-based core to complex interactive networks where non-coding RNA (ncRNA) is thought to play an essential role. As current gene ontology is based predominantly on protein-level information, there is a growing need to analyze networks with ncRNA. In this study, we propose a gene ontology workflow integrating ncRNA using the NPInter V5.0 database. To validate the proposed workflow, we analyzed our previously published curated biomarker datasets for hidden disease susceptibility processes and pharmacogenomics. Our results show a novel involvement of melanogenesis in psoriasis response to biological drugs in general. Hyperpigmentation has been previously observed in psoriasis following treatment with currently indicated biological drugs, thus calling attention to melanogenesis research as a response biomarker in psoriasis. Moreover, our proposed workflow highlights the need to critically evaluate computed ncRNA interactions within databases and a demand for gene ontology analysis of large miRNA blocks.
精心策划的在线交互数据库和基因本体论工具简化了高度复杂的基因/蛋白质网络的分析。然而，疾病发病机制的理解逐渐从基于蛋白质的核心转移到复杂的相互作用网络，其中非编码 RNA (ncRNA) 被认为起着至关重要的作用。由于当前的基因本体论主要基于蛋白质水平的信息，因此越来越需要分析包含 ncRNA 的网络。在这项研究中，我们提出了一个使用 NPInter V5.0 数据库整合 ncRNA 的基因本体论工作流程。为了验证所提出的工作流程，我们分析了我们之前发表的经过精心策划的生物标志物数据集，以发现隐藏的疾病易感性过程和药物基因组学。我们的结果表明，黑色素生成在一般情况下参与了银屑病对生物药物的反应。在目前指示的生物药物治疗后，银屑病中已经观察到色素沉着过度，因此引起了对黑色素生成研究作为银屑病反应生物标志物的关注。此外，我们提出的工作流程强调需要批判性地评估数据库中计算出的 ncRNA 相互作用，并需要对大型 miRNA 块进行基因本体论分析。
