ORCO: Ollivier-Ricci Curvature-Omics-an unsupervised method for analyzing robustness in biological systems.

Bioinformatics (Oxford, England) Pub Date : 2025-03-04 DOI:10.1093/bioinformatics/btaf093

Anish K Simhal, Corey Weistuch, Kevin Murgas, Daniel Grange, Jiening Zhu, Jung Hun Oh, Rena Elkin, Joseph O Deasy

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Abstract

Motivation: Although recent advanced sequencing technologies have improved the resolution of genomic and proteomic data to better characterize molecular phenotypes, efficient computational tools to analyze and interpret large-scale omic data are still needed.

Results: To address this, we have developed a network-based bioinformatic tool called Ollivier-Ricci curvature for omics (ORCO). ORCO incorporates omics data and a network describing biological relationships between the genes or proteins and computes Ollivier-Ricci curvature (ORC) values for individual interactions. ORC is an edge-based measure that assesses network robustness. It captures functional cooperation in gene signaling using a consistent information-passing measure, which can help investigators identify therapeutic targets and key regulatory modules in biological systems. ORC has identified novel insights in multiple cancer types using genomic data and in neurodevelopmental disorders using brain imaging data. This tool is applicable to any data that can be represented as a network.

Availability and implementation: ORCO is an open-source Python package and is publicly available on GitHub at https://github.com/aksimhal/ORC-Omics.

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Ollivier-Ricci曲率组学——一种分析生物系统鲁棒性的无监督方法。

动机：尽管最近先进的测序技术已经提高了基因组和蛋白质组数据的分辨率，以更好地表征分子表型，但仍然需要有效的计算工具来分析和解释大规模的基因组数据。结果：为了解决这个问题，我们开发了一个基于网络的生物信息学工具，称为奥利维-里奇曲率组学（ORCO）。ORCO结合了组学数据和描述基因或蛋白质之间生物关系的网络，并计算个体相互作用的奥利维-里奇曲率（ORC）值。ORC是一种基于边缘的评估网络稳健性的方法。它使用一致的信息传递措施捕获基因信号中的功能合作，这可以帮助研究人员确定生物系统中的治疗靶点和关键调节模块。ORC利用基因组数据和脑成像数据在多种癌症类型和神经发育障碍中发现了新的见解。此工具适用于任何可以表示为网络的数据。可用性：ORCO是一个开源Python包，可在GitHub上公开获取：https://github.com/aksimhal/ORC-Omics.Supplementary information：代码和笔记本可在github.com/aksimhal/ORC-Omics获得。

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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Bioinformatics (Oxford, England)

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