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

Jenjaroenpun P, Chew CS, Yong TP, Choowongkomon K, Thammasorn W, Kuznetsov VA - Nucleic Acids Res. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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A screenshot of the TTSMI database and the search results. (A) TTS search terms and basic search criteria (e.g. Gene ID 4609). (B) TTS filtering options, which are categorized into four groups: ‘Sequence context’ (sequence content of the TTS), ‘Gene region annotation’ (the TTS is located in a specific gene annotation regions), ‘Annotation tracks’ (the TTS shares a common nucleotide with the annotation tracks) and ‘Other options’ (other helpful options). (C) A close-up screenshot of TTS search results showing the current active filtering options, including gene regions and annotation tracks, as well as the paging, genome visualization and downloading buttons at the bottom. (D) Chromosome view of TTS locations (Watson strand in blue and Crick strand in red) in the human genome via the UCSC genome browser. (E) TTS information page of TTS.8.23.128748414 (the detailed information is available in Supplementary Figure S3).
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Figure 1: A screenshot of the TTSMI database and the search results. (A) TTS search terms and basic search criteria (e.g. Gene ID 4609). (B) TTS filtering options, which are categorized into four groups: ‘Sequence context’ (sequence content of the TTS), ‘Gene region annotation’ (the TTS is located in a specific gene annotation regions), ‘Annotation tracks’ (the TTS shares a common nucleotide with the annotation tracks) and ‘Other options’ (other helpful options). (C) A close-up screenshot of TTS search results showing the current active filtering options, including gene regions and annotation tracks, as well as the paging, genome visualization and downloading buttons at the bottom. (D) Chromosome view of TTS locations (Watson strand in blue and Crick strand in red) in the human genome via the UCSC genome browser. (E) TTS information page of TTS.8.23.128748414 (the detailed information is available in Supplementary Figure S3).

Mentions: The TTSMI database provides several search options for TTS searches (Figure 1A). The user can search TTSs by TTS ID, Entrez gene ID, NCBI reference sequence (refSeq) ID, chromosome location, gene symbol or gene description keywords. For example, Figure 1A illustrates a TTS search for Gene ID 4609, which represents the c-Myc gene. In addition, to increase the speed of the search, TTSs were categorized into groups based on basic search criteria for TTSs, including the guanine content (%G), number of pyrimidine interruptions and number of three consecutive guanines (GpGpG) (see Supplementary Figure S2 and Table 1).


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

Jenjaroenpun P, Chew CS, Yong TP, Choowongkomon K, Thammasorn W, Kuznetsov VA - Nucleic Acids Res. (2014)

A screenshot of the TTSMI database and the search results. (A) TTS search terms and basic search criteria (e.g. Gene ID 4609). (B) TTS filtering options, which are categorized into four groups: ‘Sequence context’ (sequence content of the TTS), ‘Gene region annotation’ (the TTS is located in a specific gene annotation regions), ‘Annotation tracks’ (the TTS shares a common nucleotide with the annotation tracks) and ‘Other options’ (other helpful options). (C) A close-up screenshot of TTS search results showing the current active filtering options, including gene regions and annotation tracks, as well as the paging, genome visualization and downloading buttons at the bottom. (D) Chromosome view of TTS locations (Watson strand in blue and Crick strand in red) in the human genome via the UCSC genome browser. (E) TTS information page of TTS.8.23.128748414 (the detailed information is available in Supplementary Figure S3).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384029&req=5

Figure 1: A screenshot of the TTSMI database and the search results. (A) TTS search terms and basic search criteria (e.g. Gene ID 4609). (B) TTS filtering options, which are categorized into four groups: ‘Sequence context’ (sequence content of the TTS), ‘Gene region annotation’ (the TTS is located in a specific gene annotation regions), ‘Annotation tracks’ (the TTS shares a common nucleotide with the annotation tracks) and ‘Other options’ (other helpful options). (C) A close-up screenshot of TTS search results showing the current active filtering options, including gene regions and annotation tracks, as well as the paging, genome visualization and downloading buttons at the bottom. (D) Chromosome view of TTS locations (Watson strand in blue and Crick strand in red) in the human genome via the UCSC genome browser. (E) TTS information page of TTS.8.23.128748414 (the detailed information is available in Supplementary Figure S3).
Mentions: The TTSMI database provides several search options for TTS searches (Figure 1A). The user can search TTSs by TTS ID, Entrez gene ID, NCBI reference sequence (refSeq) ID, chromosome location, gene symbol or gene description keywords. For example, Figure 1A illustrates a TTS search for Gene ID 4609, which represents the c-Myc gene. In addition, to increase the speed of the search, TTSs were categorized into groups based on basic search criteria for TTSs, including the guanine content (%G), number of pyrimidine interruptions and number of three consecutive guanines (GpGpG) (see Supplementary Figure S2 and Table 1).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
Related in: MedlinePlus