Vorontsov Ilya E, Fedorova Alla D, Yevshin Ivan S, Sharipov Ruslan N, Kolpakov Fedor A, Makeev Vsevolod J, Kulakovskiy Ivan V
Vavilov Institute of General Genetics, Russian Academy of Sciences, GSP-1, Gubkina 3, Moscow, Russia, 119991.
BIOSOFT.RU Ltd, Russkaya 41/1, Novosibirsk, Russia, 630058.
BMC Res Notes. 2018 Oct 23;11(1):756. doi: 10.1186/s13104-018-3856-x.
Mammalian genomics studies, especially those focusing on transcriptional regulation, require information on genomic locations of regulatory regions, particularly, transcription factor (TF) binding sites. There are plenty of published ChIP-Seq data on in vivo binding of transcription factors in different cell types and conditions. However, handling of thousands of separate data sets is often impractical and it is desirable to have a single global map of genomic regions potentially bound by a particular TF in any of studied cell types and conditions.
Here we report human and mouse cistromes, the maps of genomic regions that are routinely identified as TF binding sites, organized by TF. We provide cistromes for 349 mouse and 599 human TFs. Given a TF, its cistrome regions are supported by evidence from several ChIP-Seq experiments or several computational tools, and, as an optional filter, contain occurrences of sequence motifs recognized by the TF. Using the cistrome, we provide an annotation of TF binding sites in the vicinity of human and mouse transcription start sites. This information is useful for selecting potential gene targets of transcription factors and detecting co-regulated genes in differential gene expression data.
哺乳动物基因组学研究，尤其是那些专注于转录调控的研究，需要有关调控区域基因组位置的信息，特别是转录因子（TF）结合位点的信息。已有大量关于不同细胞类型和条件下转录因子体内结合的ChIP-Seq数据发表。然而，处理数千个单独的数据集通常不切实际，因此需要一个单一的全局图谱，显示在任何研究的细胞类型和条件下可能被特定TF结合的基因组区域。
在此，我们报告了人类和小鼠的顺反组，即按TF组织的、通常被鉴定为TF结合位点的基因组区域图谱。我们提供了349个小鼠TF和599个人类TF的顺反组。对于给定的TF，其顺反组区域得到了多个ChIP-Seq实验或多个计算工具的证据支持，并且作为一个可选的筛选条件，包含该TF识别的序列基序的出现情况。利用顺反组，我们提供了人类和小鼠转录起始位点附近TF结合位点的注释。这些信息对于选择转录因子的潜在基因靶点以及在差异基因表达数据中检测共调控基因很有用。
