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

Z Zou, T Ohta, F Miura, S Oki - Nucleic acids research, 2022 - academic.oup.com
… This epigenomic landscape can also be characterized for multiple genes and genomic loci
by … Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All …

ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data

Z Zou, T Ohta, S Oki - Nucleic Acids Research, 2024 - academic.oup.com
epigenomic landscapes, powered by the comprehensive integration of over 376 000 public
ChIP-… ChIP-Atlas 3.0 that enhances clarity by incorporating additional tracks for genomic and …

[HTML][HTML] Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses

Z Zou, M Iwata, Y Yamanishi, S Oki - BMC bioinformatics, 2022 - Springer
… In summary, CTD, ChIP-Atlas, and DisGeNET include information about biologically significant
genes and proteins, and are therefore suitable for elucidating the MoAs of chemicals and …

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

A Griffon, Q Barbier, J Dalino, J van Helden… - Nucleic acids …, 2015 - academic.oup.com
… Here, we report the complex landscape of TFBS in the human genome. We have constructed
a global map of regulatory elements by compiling the genomic localization of 132 different …

[HTML][HTML] An epigenome atlas of neural progenitors within the embryonic mouse forebrain

CT Rhodes, JJ Thompson, A Mitra, D Asokumar… - Nature …, 2022 - nature.com
… It is well established that changes in a cell’s epigenetic landscape alter cell fate decisions
… Thus, a thorough characterization of the epigenomic landscape during neurogenesis is …

[HTML][HTML] A unique epigenomic landscape defines human erythropoiesis

VP Schulz, H Yan, K Lezon-Geyda, X An, J Hale… - Cell reports, 2019 - cell.com
Epigenomic landscape of erythropoiesis reveals stage-… The epigenome of terminally
differentiating erythroid cells … These epigenomic and transcriptome data are powerful tools to …

An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses

M Wang, Z Li, Y Zhang, Y Zhang, Y Xie, L Ye… - The Plant …, 2021 - academic.oup.com
… gene expression based on RE epigenome between epigenome correlation method and the
… We herein characterized the epigenomic architecture in a large spectrum of samples, and …

The chromatin accessibility landscape of primary human cancers

…, C Curtis, Cancer Genome Atlas Analysis Network†… - Science, 2018 - science.org
… Nonetheless, the gene regulatory landscapes of these tumors have largely been inferred …
samples from TCGA, identifying diverse regulatory landscapes across 23 cancer types. These …

[HTML][HTML] Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain

A Dincer, DP Gavin, K Xu, B Zhang, JT Dudley… - Translational …, 2015 - nature.com
… As a quality control and validation of ChIP-seq experiments, we compiled the H3K4me3
epigenomic landscape patterns for RefSeq-annotated genes across all samples and computed …

[HTML][HTML] Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks

AF Rendeiro, C Schmidl, JC Strefford… - Nature …, 2016 - nature.com
… To provide a basis for studying epigenome deregulation in CLL, here we present genome-…
in the chromatin landscape of CLL, established a community resource for studying epigenome