Review of ChIP-Atlas was published in JSBi Bioinformatics Review

  • Others
  • Funding
  • Database Integration Coordination Program
Jun 6, 2023

A review of ChIP-Atlas developed by Shinya OKI, Associate Professor of Kyoto University, and his colleagues, has been published in JSBi Bioinformatics Review. In this article, an overview of ChIP-Atlas and case studies of research conducted with ChIP-Atlas in the areas of drug discovery, regenerative medicine and genetic diseases.

  • This article provides the following case studies.
  • 1) Case study that led to the identification of a master transcription factor that integrally regulates a group of genes that respond to drug perturbations, including cisplatin, leflunomide, and valproic acid.
  • 2) Case study that inferred a combination of pioneer and cooperating factors that direct reprogramming from fibroblasts to hepatocytes, chondrocytes, neurons, cardiomyocytes, pancreatic cells, and small intestinal panate cells.
  • 3) Case study that suggested ESRRG, an orphan nuclear receptor, to regulate the expression of the ion channel and sarcomere component gene clusters in the myocardium and to be involved in the development of atrial fibrillation.

Using ChIP-Atlas, it is possible to identify master transcription factors that regulate the expression of a specific gene cluster, or to narrow down the candidates of important transcription factors involved in cell differentiation or disease development, as described in this article.

For details, see "ChIP-Atlas - Walking the Transcriptional Regulatory Landscape" JSBi Bioinformatics Review, 4(1), 1-9 (2023).

ChIP-Atlas is developed and operated as a part of "INTRARED", which is being developed in "Construction of an integrative data platform for transcriptional regulations" (PI: Takeya KASUKAWA) funded by "Database Integration Coordination Program (DICP)".

Contents of ChIP-Atlas(June 5,2023)

  • ChIP-seq 219,830 experiments
  • ATAC-seq 82,757 experiments
  • DNase-seq 6,380 experiments
  • Bisulfite-seq 55,030 experiments

Total 363,997 experiments

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