Thomas Zachary V, Wang Zhenjia, Zang Chongzhi
Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
NAR Cancer. 2021 Mar 22;3(1):zcab011. doi: 10.1093/narcan/zcab011. eCollection 2021 Mar.
Dysregulation of gene expression plays an important role in cancer development. Identifying transcriptional regulators, including transcription factors and chromatin regulators, that drive the oncogenic gene expression program is a critical task in cancer research. Genomic profiles of active transcriptional regulators from primary cancer samples are limited in the public domain. Here we present BART Cancer (bartcancer.org), an interactive web resource database to display the putative transcriptional regulators that are responsible for differentially regulated genes in 15 different cancer types in The Cancer Genome Atlas (TCGA). BART Cancer integrates over 10000 gene expression profiling RNA-seq datasets from TCGA with over 7000 ChIP-seq datasets from the Cistrome Data Browser database and the Gene Expression Omnibus (GEO). BART Cancer uses Binding Analysis for Regulation of Transcription (BART) for predicting the transcriptional regulators from the differentially expressed genes in cancer samples compared to normal samples. BART Cancer also displays the activities of over 900 transcriptional regulators across cancer types, by integrating computational prediction results from BART and the Cistrome Cancer database. Focusing on transcriptional regulator activities in human cancers, BART Cancer can provide unique insights into epigenetics and transcriptional regulation in cancer, and is a useful data resource for genomics and cancer research communities.
基因表达失调在癌症发展中起着重要作用。识别驱动致癌基因表达程序的转录调节因子，包括转录因子和染色质调节因子，是癌症研究中的一项关键任务。来自原发性癌症样本的活性转录调节因子的基因组图谱在公共领域有限。在这里，我们展示了BART Cancer（bartcancer.org），这是一个交互式网络资源数据库，用于展示负责《癌症基因组图谱》（TCGA）中15种不同癌症类型中差异调节基因的推定转录调节因子。BART Cancer将来自TCGA的10000多个基因表达谱RNA测序数据集与来自Cistrome数据浏览器数据库和基因表达综合数据库（GEO）的7000多个染色质免疫沉淀测序（ChIP-seq）数据集整合在一起。BART Cancer使用转录调控结合分析（BART）来预测癌症样本与正常样本相比差异表达基因中的转录调节因子。通过整合BART和Cistrome癌症数据库的计算预测结果，BART Cancer还展示了900多种转录调节因子在不同癌症类型中的活性。专注于人类癌症中的转录调节因子活性，BART Cancer可以为癌症中的表观遗传学和转录调控提供独特的见解，并且是基因组学和癌症研究社区的有用数据资源。
