CistromeFinder 可重复使用于 ChIP-seq 和 DNase-seq 数据。
CistromeFinder for ChIP-seq and DNase-seq data reuse.
机构信息
Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 20092, China.
出版信息
Bioinformatics. 2013 May 15;29(10):1352-4. doi: 10.1093/bioinformatics/btt135. Epub 2013 Mar 18.
SUMMARY
Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We created a data portal CistromeFinder that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations. Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.
AVAILABILITY
CONTACT
摘要
尽管对于实验生物学家社区来说，数据再利用具有挑战性，但利用染色质免疫沉淀和高通量测序的 DNA 酶 I 超敏反应检测极大地加速了对转录和表观遗传调控的理解。我们创建了一个名为 CistromeFinder 的数据门户，可帮助查询、评估和可视化人类和小鼠中公开的染色质免疫沉淀和高通量测序数据的 DNA 酶 I 超敏反应检测。该数据库目前包含 4391 个数据集的 6378 个样本、313 个因子和 102 个细胞系或细胞群。每个数据集都经过了一致的分析和质量控制流程；因此，用户可以在检查感兴趣基因附近的结合位点之前，评估每个数据集的整体质量。CistromeFinder 与 UCSC 基因组浏览器集成，用于可视化，与 Primer3Plus 一起用于 ChIP-qPCR 引物设计，与 CistromeMap 一起用于提交新的可用数据集。它还允许用户发表评论，以促进数据评估和更新。
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