Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse
By S. Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxi Wu, Xiaohui Shi, Len Taing and 4 more. Nucleic Acids Res., 2016
505 citations recorded by the source corpus.
Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/68bd3de081d1baa8df24bec6ec2ad46df5e48b6c
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In Molecular Biology
Citations in the corpus
- ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments (2017, methodology): “As the quality of ChIP-seq experiments vary significantly (20,21), we incorporated a critical data quality filtering step in our pipeline––not implemented in other databases (chip-atlas http://chip-atlas.org (6,7,18)).”
- hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets (2019, unknown): “Additionally, although CistromeDB can search TF-target regulations for a single query gene and browse peak information of a given TF, it ignores the co-regulation information for TF-targets, and does not refer to the TF-target regulations at the genome-wide level.”
- Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, methodology): “We reported the first version of the Cistrome DB in the 2017 Nucleic Acids Research database issue (19).”
- PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants (2018, background): “To date, several databases have been developed to explore the occupancy landscapes of regulatory factors, such as, Cistrome DB (4), ReMap (5), Factorbook (6), GTRD (7), PlantTFDB (8), ChIPBase (9) and Expresso (10).”