LiqBiMark: An advanced bioinformatics pipeline for integrative transcriptomic analysis and identification of non-invasive prognostic biomarkers using GEO datasets

IF 0.9 Q4 GENETICS & HEREDITY

Human Gene Pub Date : 2025-12-01 Epub Date: 2025-09-29 DOI:10.1016/j.humgen.2025.201490

Amir Mohammad Mazhari , Farshad Safaei , Mahsa Torkamanian-Afshar , Ali Najafi

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Abstract

Background

The Gene Expression Omnibus (GEO) database was established by the National Center for Biotechnology Information (NCBI) to facilitate sharing molecular biology data. This repository hosts numerous datasets related to complex diseases such as cancer, generated by researchers worldwide. One of the most challenging issues is finding non-invasive biomarkers in the vast amount of data deposited in public databases related to a specific type of cancer.

Results

To address this issue, we have designed a Liquid Biopsy Biomarker Discovery (LiqBiMark) pipeline that compares two datasets on the same type of cancer, but with different sample sources, to propose potential biomarker candidates. Additionally, the LiqBiMark generates co-expression networks and conducts clustering analysis.

Conclusions

The pipeline is designed to be accessible even to users with minimal experience, allowing them to obtain results quickly and efficiently.

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LiqBiMark：一个先进的生物信息学管道，用于整合转录组学分析和使用GEO数据集鉴定非侵入性预后生物标志物

GEO （Gene Expression Omnibus）数据库是由美国国家生物技术信息中心（NCBI）为促进分子生物学数据共享而建立的。该存储库拥有由世界各地的研究人员生成的与癌症等复杂疾病相关的大量数据集。最具挑战性的问题之一是在与特定类型癌症相关的公共数据库中存储的大量数据中找到非侵入性生物标志物。为了解决这个问题，我们设计了一个液体活检生物标志物发现（Liquid Biopsy Biomarker Discovery, LiqBiMark）管道，该管道比较了同一类型癌症的两个数据集，但具有不同的样本来源，以提出潜在的生物标志物候选物。此外，LiqBiMark生成共表达网络并进行聚类分析。结论：该管道的设计即使对经验最少的用户也是可访问的，使他们能够快速有效地获得结果。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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