Discovery of novel biomarkers with extended non-coding RNA interactor networks from genetic and protein biomarkers

Jezernik, Gregor (author), Glavač, Damjan (author), Skok, Pavel (author), Krušič, Martina (author), Potočnik, Uroš (author), Gorenjak, Mario (author)

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.

• Language: English
• Keywords: disease pathogenesis, gene ontology, untranslated RNA, biomarkers, non-coding RNA
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 16 str.
• Numbering: Vol. 25, iss. 18, art. 10210
• PID: 20.500.12556/RUL-169396
• UDC: 575
• ISSN on article: 1422-0067
• DOI: 10.3390/ijms251810210
• COBISS.SI-ID: 208743939
• Publication date in RUL: 27.05.2025

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.