User profiles for H. Kawaji

Hideya Kawaji

Tokyo Metropolitan Institute of Medical Science
Verified email at igakuken.or.jp
Cited by 28992

The systems biology graphical notation

…, FT Bergman, R Gauges, P Ghazal, H Kawaji… - Nature …, 2009 - nature.com
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard
visual languages that help accelerate work by promoting regularity, removing ambiguity …

An atlas of active enhancers across human cell types and tissues

…, TF Meehan, T Lassmann, M Itoh, H Kawaji… - Nature, 2014 - nature.com
… A second hit of 22 nM siRNA was given after 48 h. Cells were collected an additional 48
h after the second hit, and protein depletion was verified by western blotting analysis as …

Genome-wide analysis of mammalian promoter architecture and evolution

…, Y Kitazume, H Kawaji, C Kai, M Nakamura, H Konno… - Nature …, 2006 - nature.com
… 0.01, Kruskal-Willis test) for which we currently have sufficient tags to make assessments (H.
Kawaji et al., data not shown). CpG island promoter regions are also commonly associated …

Enhanced identification of transcriptional enhancers provides mechanistic insights into diseases

…, H Kawaji, M Nishikawa, H Zayed, H Suzuki… - Trends in Genetics, 2016 - cell.com
Enhancers are distal cis-regulatory DNA elements that increase the expression of target
genes. Various experimental and computational approaches including chromatin signature …

An atlas of human long non-coding RNAs with accurate 5′ ends

…, S Schmeier, TM Poulsen, J Severin, M Lizio, H Kawaji… - Nature, 2017 - nature.com
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized.
Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate …

[HTML][HTML] Gateways to the FANTOM5 promoter level mammalian expression atlas

…, P Carninci, Y Hayashizaki, ARR Forrest, H Kawaji… - Genome biology, 2015 - Springer
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human
and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of …

The BioMart community portal: an innovative alternative to large, centralized data repositories

…, S Hu, ZL Hu, L Hutchins, Z Kan, H Kawaji… - Nucleic acids …, 2015 - academic.oup.com
The BioMart Community Portal ( www.biomart.org ) is a community-driven effort to provide a
unified interface to biomedical databases that are distributed worldwide. The portal provides …

[HTML][HTML] An atlas of combinatorial transcriptional regulation in mouse and man

…, W Hide, O Hofmann, A Kamburov, M Kaur, H Kawaji… - Cell, 2010 - cell.com
Combinatorial interactions among transcription factors are critical to directing tissue-specific
gene expression. To build a global atlas of these combinations, we have screened for …

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

…, K Waki, T Kasukawa, H Kawaji… - Proceedings of the …, 2003 - National Acad Sciences
… in 100 μl, and incubated at 37C for 1 h. After Proteinase K treatment, samples were phenol/…
16C for 16 h. Heating the reaction mixture at 65C for 5 min terminated the ligation reaction. …

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

…, T Kasukawa, T Lassmann, H Suzuki, H Kawaji… - Science, 2015 - science.org
Although it is generally accepted that cellular differentiation requires changes to transcriptional
networks, dynamic regulation of promoters and enhancers at specific sets of genes has …