Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA.

IF 3.7 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2025-07-01 DOI:10.1186/s12864-025-11747-y

Aurora Savino, Raffaele M Iannuzzi, Lidia Avalle, Andrea Lobascio, Francesco Iorio, Paolo Provero, Valeria Poli

引用次数: 0

Abstract

Background: Understanding the molecular interactions between cells, tissues or organs is key to understanding the functioning of a biological system as a whole.

Results: Here, we propose crossWGCNA: a co-expression-based method that identifies highly interacting genes unbiasedly and that we employ to study stroma-epithelium communication in breast cancer. CrossWGCNA can be applied to bulk, single cell and spatial transcriptomics data. We validate it both in silico and experimentally, and we provide a fully documented R package allowing users to employ it.

Conclusions: The wide applicability and agnostic nature of our tool make it complementary to existing methods overcoming the limitations arising from strong baseline assumptions.

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跨组织基因表达的相互作用从大块，单细胞和空间转录组与交叉gcna。

背景：了解细胞、组织或器官之间的分子相互作用是理解整个生物系统功能的关键。结果：在这里，我们提出了cross - swgcna：一种基于共表达的方法，可以无偏地识别高度相互作用的基因，我们将其用于研究乳腺癌基质-上皮间质通讯。crossswgcna可用于批量、单细胞和空间转录组学数据。我们在计算机和实验中验证了它，并提供了一个完整的文档R包，允许用户使用它。结论：我们的工具的广泛适用性和不可知论性质使其成为现有方法的补充，克服了由强基线假设引起的局限性。

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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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.