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The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast
- Source :
- BMC Genomics
- Publication Year :
- 2014
- Publisher :
- BioMed Central, 2014.
-
Abstract
- Histone modification and remodeling play crucial roles in regulating gene transcription. These post-translational modifications of histones function in a combinatorial fashion and can be recognized by specific histone-binding proteins, thus regulating gene transcription. Therefore, understanding the combinatorial patterns of the histone code is vital to understanding the associated biological processes. However, most of the datasets regarding histone modification and chromatin regulation are scattered across various studies, and no comprehensive search and query tool has yet been made available to retrieve genes bearing specific histone modification patterns and regulatory proteins. For this reason, we developed the Yeast Nucleosome Atlas database, or the YNA database, which integrates the available experimental data on nucleosome occupancy, histone modifications, the binding occupancy of regulatory proteins, and gene expression data, and provides the genome-wide gene miner to retrieve genes with a specific combination of these chromatin-related datasets. Moreover, the biological significance analyzer, which analyzes the enrichments of histone modifications, binding occupancy, transcription rate, and functionality of the retrieved genes, was constructed to help researchers to gain insight into the correlation among chromatin regulation and transcription. Compared to previously established genome browsing databases, YNA provides a powerful gene mining and retrieval interface, and is an investigation tool that can assist users to generate testable hypotheses for studying chromatin regulation during transcription. YNA is available online at http://cosbi3.ee.ncku.edu.tw/yna/ .
- Subjects :
- Nucleosome Occupancy
Genes, Fungal
Saccharomyces cerevisiae
Biology
computer.software_genre
Chromatin remodeling
Histones
User-Computer Interface
Databases, Genetic
Transcriptional regulation
Genetics
Histone code
Nucleosome
Data Mining
Transcription Regulation
Epigenomics
Database
Histone Modifications
Research
Gene Expression Profiling
Molecular Sequence Annotation
Chromatin
Regulatory Proteins
Nucleosomes
Gene expression profiling
Histone
Chromatin Regulation
Mutation
biology.protein
computer
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 15
- Issue :
- Suppl 9
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....25b2a1cbb76b9a2761e67db7e7ecedc9