ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Abstract

ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape. ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein–genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.

CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana

“…In a benchmark study ( Thomas et al, 2017 ) MACS2 peak caller outperformed GEM in terms of sensitivity and precision. The MACS2 is the most popular and the sole peak caller that has been applied in all basic whole-genome TF binding profile annotation databases, e.g., ReMap ( Hammal et al, 2022 ), CISTROME DB ( Zheng et al, 2019 ), ChIP-Atlas ( Zou et al, 2022 ), and GTRD ( Kolmykov et al, 2021 ). What is important for the gene list enrichment analysis, MACS2 uses the windows of multiple widths to scan a genome for candidate peaks and produces a set of peaks with carefully adjusted lengths.…”

Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression

“…Future developments of DEET would extend its database to searchable, consistently analyzed, and curated differential expression analyses collected from multiple species in Expression Atlas (27). Lastly, extending DEET to be able to search differential comparisons derived from consistent experiments beyond RNA-seq would be a logical next step to harness ongoing efforts for systematic analysis of public data from different genomic techniques such as scRNA-seq (20,77), accessible chromatin profiling (ATACseq/DNAse-seq) (78,79), and protein-DNA interactions mapping (ChIP-seq and in the future CUT&RUN/TAG) (80)(81)(82)(83). In summary, by allowing users to rapidly connect their gene lists to a curated set of uniformly processed differential gene expression analyses, tools like DEET will facilitate access to the treasure trove of public RNA-seq data.…”

Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets

“…Identification of ChIP-seq data was predominantly facilitated using the Chip Atlas database (Zou et al, 2022) owing to its breadth of mouse and human data and the organization of the associated metadata. Additional experiments were identified in the literature and other ChIP-seq resources: GTRD (Kolmykov et al, 2021), Unibind (Puig et al, 2021), and Cistromedb (Zheng et al, 2018).…”