SNP2TFBS-a database of regulatory SNPs affecting predicted transcription factor binding site affinity

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D139-D144

  Kumar, Sunil ^a,b   Ambrosini, Giovanna ^a,b   Bucher, Philipp ^a,b  

^a EPFL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; PROTEIN BINDING;

ALGORITHM; ALLELE; ARTICLE; BINDING AFFINITY; BINDING SITE; GENETIC DATABASE; GENOTYPE; HETEROZYGOTE; HUMAN GENOME; POSITION WEIGHT MATRIX; PREDICTION; PROBABILITY; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; GENOMICS; HUMAN; METABOLISM; NUCLEIC ACID DATABASE; PROCEDURES; WEB BROWSER;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOME, HUMAN; GENOMICS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; TRANSCRIPTION FACTORS; WEB BROWSER;

EID: 85016148342     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1064     Document Type: Article

References (20)

1. Hrdlickova, B., de Almeida, R.C., Borek, Z. and Withoff, S. (2014) Genetic variation in the non-coding genome: involvement of micro-RNAs and long non-coding RNAs in disease. Biochim. et Biophys. Acta, 1842, 1910-1922.
2. Farh, K.K., Marson, A., Zhu, J., Kleinewietfeld, M., Housley, W.J., Beik, S., Shoresh, N., Whitton, H., Ryan, R.J., Shishkin, A.A. et al. (2015) Genetic and epigenetic fne mapping of causal autoimmune disease variants. Nature, 518, 337-343.
3. Pai, A.A., Pritchard, J.K. and Gilad, Y. (2015) The genetic and mechanistic basis for variation in gene regulation. PLoS Genet., 11, e1004857.
4. Zuo, C., Shin, S. and Keles, S. (2015) atSNP: transcription factor binding affnity testing for regulatory SNP detection. Bioinformatics, 31, 3353-3355.
5. Thomas-Chollier, M., Hufton, A., Heinig, M., O'Keeffe, S., Masri, N.E., Roider, H.G., Manke, T. and Vingron, M. (2011) Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat. Protoc., 6, 1860-1869.
6. Coetzee, S.G., Coetzee, G.A. and Hazelett, D.J. (2015) motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics, 31, 3847-3849.
7. Andersen, M.C., Engstrom, P.G., Lithwick, S., Arenillas, D., Eriksson, P., Lenhard, B., Wasserman, W.W. and Odeberg, J. (2008) In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol., 4, e5.
8. Riva, A. (2012) Large-scale computational identifcation of regulatory SNPs with rSNP-MAPPER. BMC Genomics, 13(Suppl. 4), S7.
9. Perera, D., Chacon, D., Thoms, J.A., Poulos, R.C., Shlien, A., Beck, D., Campbell, P.J., Pimanda, J.E. and Wong, J.W. (2014) OncoCis: annotation of cis-regulatory mutations in cancer. Genome Biol., 15, 485.
10. Ward, L.D. and Kellis, M. (2016) HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res., 44, D877-D881.
11. Wu, J. and Xie, J. (2010) Hidden Markov model and its applications in motif fndings. Methods Mol. Biol., 620, 405-416.
12. Mathelier, A., Fornes, O., Arenillas, D.J., Chen, C.Y., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R. et al. (2016) JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profles. Nucleic Acids Res., 44, D110-D115.
13. Wang, K., Li, M. and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
14. O'Leary, N.A., Wright, M.W., Brister, J.R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D. et al. (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res., 44, D733-D745.
15. Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N. et al. (2011) AlleleSeq: analysis of allele-specifc expression and binding in a network framework. Mol. Syst. Biol., 7, 522.
16. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
17. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and Genome Project Data Processing, S. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
18. Jin, W., Goldfne, A.B., Boes, T., Henry, R.R., Ciaraldi, T.P., Kim, E.Y., Emecan, M., Fitzpatrick, C., Sen, A., Shah, A. et al. (2011) Increased SRF transcriptional activity in human and mouse skeletal muscle is a signature of insulin resistance. J. Clin. Invest., 121, 918-929.
19. Macintyre, G., Bailey, J., Haviv, I. and Kowalczyk, A. (2010) is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics, 26, i524-i530.
20. Boyle, A.P., Hong, E.L., Hariharan, M., Cheng, Y., Schaub, M.A., Kasowski, M., Karczewski, K.J., Park, J., Hitz, B.C., Weng, S. et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res., 22, 1790-1797.