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Nucleic Acids Res. 2015 Jan;43(Database issue):D110-6. doi: 10.1093/nar/gku970. Epub 2014 Oct 16.

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.

Author information

1
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore Interdisciplinary Graduate Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkean, Bangkok 10900, Thailand.
2
Open source Computing and Technology Innovation, Bioinformatics Institute, 138671, Singapore.
3
Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak, Bangkok 10900, Thailand.
4
Bioinformatics and Systems Biology Program, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd, Tha Kham, Bangkok 10150, Thailand.
5
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore vladimirk@bii.a-star.edu.sg.

Abstract

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser.

PMID:
25324314
PMCID:
PMC4384029
DOI:
10.1093/nar/gku970
[Indexed for MEDLINE]
Free PMC Article

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