Cao Zhipeng, Bao Li, Qin Jinmei, Zhan Guilai
Shanghai Xuhui Mental Health Center, Shanghai, China.
School of Mental Health, Wenzhou Medical University, Zhejiang Province, China.
Biol Psychiatry Glob Open Sci. 2025 Jul 18;5(6):100568. doi: 10.1016/j.bpsgos.2025.100568. eCollection 2025 Nov.
Imaging transcriptomics integrates spatial gene expression data with imaging-derived phenotypes (IDPs) to elucidate molecular mechanisms that underlie brain structure and function. Overrepresentation analysis (ORA) is widely used to annotate IDP-related genes; however, many studies have overlooked appropriate background gene selection. Here, we critically evaluated the impact of omitting a proper background on ORA findings. A systematic review of 152 imaging transcriptomics studies (2015-2024) revealed that 84.9% did not report background genes, and only 5.26% used the Allen Human Brain Atlas (AHBA) genes as background. Simulations showed that ORA significance increased with background size. In realistic simulations, default backgrounds (e.g., all protein-coding genes) inflated pathway significance by up to 50-fold, with probabilities reaching 0.97, particularly for frequently reported pathways related to synaptic signaling and neurotransmission. In contrast, using AHBA genes as the background maintained the significance probabilities near 0.05. These findings highlight the need for appropriate background selection and transparent reporting and we provide practical guidance for ORA in imaging transcriptomics.
影像转录组学将空间基因表达数据与影像衍生表型（IDP）相结合，以阐明构成脑结构和功能基础的分子机制。过表达分析（ORA）被广泛用于注释与IDP相关的基因；然而，许多研究忽略了合适的背景基因选择。在此，我们批判性地评估了省略合适背景对ORA结果的影响。对152项影像转录组学研究（2015 - 2024年）的系统综述显示，84.9%的研究未报告背景基因，只有5.26%的研究使用艾伦人类大脑图谱（AHBA）基因作为背景。模拟结果表明，ORA的显著性随背景大小增加。在实际模拟中，默认背景（如所有蛋白质编码基因）会使通路显著性膨胀高达50倍，概率达到0.97，特别是对于频繁报道的与突触信号传导和神经传递相关的通路。相比之下，使用AHBA基因作为背景可使显著性概率维持在0.05左右。这些发现凸显了进行合适背景选择和透明报告的必要性，并且我们为影像转录组学中的ORA提供了实用指南。
