Aghamirzaie Delasa, Raja Velmurugan Karthik, Wu Shuchi, Altarawy Doaa, Heath Lenwood S, Grene Ruth
Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA, 24061, USA.
Center for Bioinformatics and Genetics and the Primary Care Research Network, Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA.
F1000Res. 2017 Mar 28;6:372. doi: 10.12688/f1000research.10041.1. eCollection 2017.
The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. We present Expresso (database and webserver) as a tool for the collection and integration of available ChIP-Seq peak data, which in turn can be linked to a user's gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/.
染色质免疫沉淀测序（ChIP-Seq）数据越来越容易获取，这使我们能够更多地了解转录因子在基因表达调控中的作用。尽管转录调控通常涉及多个转录因子的协同作用，但每个单独的ChIP-Seq数据集的格式通常代表单个转录因子的作用。因此，一个精心管理可用ChIP-Seq数据集的关系数据库至关重要。我们展示了Expresso（数据库和网络服务器），它是一种用于收集和整合可用ChIP-Seq峰值数据的工具，这些数据又可以与用户的基因表达数据相链接。通过对公开可用的GEO ChIP-Seq数据集进行基序分析，确定了转录因子的已知靶基因。Expresso目前提供三项服务：1）识别给定转录因子的靶基因；2）识别调控感兴趣基因的转录因子；3）计算转录因子及其靶基因的基因表达之间的相关性。可在http://bioinformatics.cs.vt.edu/expresso/免费获取Expresso。
