Lavrekha Viktoriya V, Levitsky Victor G, Tsukanov Anton V, Bogomolov Anton G, Grigorovich Dmitry A, Omelyanchuk Nadya, Ubogoeva Elena V, Zemlyanskaya Elena V, Mironova Victoria
Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
Front Plant Sci. 2022 Aug 18;13:942710. doi: 10.3389/fpls.2022.942710. eCollection 2022.
Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for genes.
拥有足够数量的基因组编码转录因子（TF）的DNA结合图谱，为系统评估基因列表的上游调节因子开辟了前景。植物顺式作用元件数据库是使用DAP-seq方法检测到的大量TF结合图谱的集合，这使得拟南芥成为可能。在这里，我们使用MACS2对原始DAP-seq数据进行了重新处理，MACS2是最受欢迎的峰调用工具，根据质量指标在其他工具中领先。在基准研究中，我们证实改进后的TF结合图谱集合支持更精确的基因列表富集程序，并导致潜在上游调节因子的排名更相关。此外，我们一致地找回了先前DAP-seq峰集集合中缺失的TF结合图谱。我们开发了CisCross网络服务（https://plamorph.sysbio.ru/ciscross/），该服务在分析基因潜在上游TF调节因子时提供了更大的灵活性。
