Protocol for Predicting the Single-Cell Network-Based Gene Activity Landscape During Human B Cell Development

Xin Huang, Xuetong Hou, Yizhen Li,Jun J Yang,Jiyang Yu

STAR protocols（2025）

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Abstract

Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. We describe steps for acquiring bone marrow data; conducting single-cell downstream analysis; and leveraging the St. Jude Algorithm for the Reconstruction of Accurate Cellular Networks (SJARACNe), Network-based Bayesian Inference of Drivers (NetBID2), and single-cell Mutual Information-based Network Engineering Ranger (scMINER) algorithms for network-based analysis. Our protocol elucidates the biological characteristics of developmental stages in human B cells. For complete details on the use and execution of this protocol, please refer to Huang et al.1.

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Key words

bioinformatics,immunology,single Cell,systems biology

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【要点】：本研究提出一种构建人类B细胞发育阶段基因调控网络和基因活动景观的协议，旨在解决B细胞分类不一致性和亚群区分困难的问题。

【方法】：通过获取骨髓数据，执行单细胞下游分析，并应用SJARACNe、NetBID2和scMINER算法进行网络分析来揭示B细胞发育阶段的生物学特征。

【实验】：研究具体步骤未详述，但提到使用骨髓数据集，通过上述方法分析得到B细胞发育各阶段的基因调控网络和活动景观，具体结果请参见Huang等的研究。