利用PageRank算法在基因调控网络中对转录因子进行优先级排序。
Prioritizing transcriptional factors in gene regulatory networks with PageRank.
作者信息
Ding Hongxu, Yang Ying, Xue Yuanqing, Seninge Lucas, Gong Henry, Safavi Rojin, Califano Andrea, Stuart Joshua M
机构信息
Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Department of Systems Biology, Columbia University, New York, NY, USA.
出版信息
iScience. 2020 Dec 30;24(1):102017. doi: 10.1016/j.isci.2020.102017. eCollection 2021 Jan 22.
Biological states are controlled by orchestrated transcriptional factors (TFs) within gene regulatory networks. Here we show TFs responsible for the dynamic changes of biological states can be prioritized with temporal PageRank. We further show such TF prioritization can be extended by integrating gene regulatory networks reverse engineered from multi-omics profiles, e.g. gene expression, chromatin accessibility, and chromosome conformation assays, using multiplex PageRank.
生物状态由基因调控网络中精心编排的转录因子（TFs）控制。在此，我们表明负责生物状态动态变化的转录因子可以通过时间PageRank算法进行优先级排序。我们进一步表明，通过使用多重PageRank算法整合从多组学图谱（如基因表达、染色质可及性和染色体构象分析）反向工程得到的基因调控网络，这种转录因子优先级排序可以得到扩展。
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