Jiang C, Xuan Z, Zhao F, Zhang M Q
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring, Harbor NY 11724, USA.
Nucleic Acids Res. 2007 Jan;35(Database issue):D137-40. doi: 10.1093/nar/gkl1041.
Transcriptional factors (TFs) and many of their target genes are involved in gene regulation at the level of transcription. To decipher gene regulatory networks (GRNs) we require a comprehensive and accurate knowledge of transcriptional regulatory elements. TRED (http://rulai.cshl.edu/TRED) was designed as a resource for gene regulation and function studies. It collects mammalian cis- and trans-regulatory elements together with experimental evidence. All the regulatory elements were mapped on to the assembled genomes. In this new release, we included a total of 36 TF families involved in cancer. Accordingly, the number of target promoters and genes for TF families has increased dramatically. There are 11,660 target genes (7479 in human, 2691 in mouse and 1490 in rat) and 14,908 target promoters (10,225 in human, 2985 in mouse and 1698 in rat). Additionally, we constructed GRNs for each TF family by connecting the TF-target gene pairs. Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research.
转录因子（TFs）及其许多靶基因参与转录水平的基因调控。为了解析基因调控网络（GRNs），我们需要全面且准确地了解转录调控元件。TRED（http://rulai.cshl.edu/TRED）被设计为一个用于基因调控和功能研究的资源库。它收集了哺乳动物的顺式和反式调控元件以及实验证据。所有调控元件都已映射到组装好的基因组上。在这个新版本中，我们总共纳入了36个与癌症相关的TF家族。相应地，TF家族的靶启动子和基因数量大幅增加。有11,660个靶基因（人类7479个、小鼠2691个、大鼠1490个）和14,908个靶启动子（人类10,225个、小鼠2985个、大鼠1698个）。此外，我们通过连接TF - 靶基因对为每个TF家族构建了基因调控网络。TF与其靶基因之间的这种相互作用数据将有助于详细的功能研究，并有助于全面了解癌症研究中的基因调控网络。
