Hansen Jens, Iyengar Ravi
Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
Bioinform Adv. 2025 Aug 18;5(1):vbaf197. doi: 10.1093/bioadv/vbaf197. eCollection 2025.
Advances in high-throughput technologies have shifted the focus from bulk to single cell or spatial transcriptomic and proteomic analysis of tissues and cell cultures. The resulting increase in gene and/or protein lists leads to the subsequent growth of up- and downregulated pathways lists. This trend creates the need for pathway-network based integration strategies that allow quick exploration of shared and distinct mechanisms across datasets.
Here, we present Molecular Biology of the Cell (MBC) Pathway Networks (PathNet). MBC PathNet allows for quick and easy integration and visualization of networks of functionally related pathways predicted from gene and protein lists using the Molecular Biology of the Cell Ontology and other ontologies. Within networks of hierarchical parent-child relationships or functional relationships, pathways are visualized as pie charts where each slice represents a dataset that predicted that pathway. Sizes of pies and slices can be selected to represent statistical significance or other quantitative measures. In addition, MBC PathNet can generate bar diagrams, heatmaps, and timelines. Fully automated execution from the command line is supported.
iyengarlab.org/mbcpathnet; mbc-ontology.org; github.com/SBCNY/Molecular-Biology-of-the-Cell.
高通量技术的进步已将研究重点从组织和细胞培养物的整体分析转移到单细胞或空间转录组学和蛋白质组学分析。由此产生的基因和/或蛋白质列表的增加导致上调和下调通路列表随之增长。这种趋势产生了对基于通路网络的整合策略的需求，该策略能够快速探索跨数据集的共享和独特机制。
在此，我们展示了《细胞分子生物学》（MBC）通路网络（PathNet）。MBC PathNet允许使用《细胞分子生物学本体论》和其他本体论，对从基因和蛋白质列表预测的功能相关通路网络进行快速简便的整合和可视化。在具有层次父子关系或功能关系的网络中，通路以饼图形式可视化，其中每个切片代表预测该通路的一个数据集。可以选择饼图和切片的大小来表示统计显著性或其他定量指标。此外，MBC PathNet可以生成条形图、热图和时间线。支持从命令行进行全自动执行。
iyengarlab.org/mbcpathnet；mbc-ontology.org；github.com/SBCNY/Molecular-Biology-of-the-Cell。
