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Volumn 43, Issue 21, 2015, Pages

BayesPI-BAR: A new biophysical model for characterization of regulatory sequence variations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; BAYESPI BAR MODEL; BINDING AFFINITY; CONTROLLED STUDY; DNA SEQUENCE; GENE FREQUENCY; HUMAN; IS RSNP MODEL; MEASUREMENT ACCURACY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA INTERACTION; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STRAP MODEL; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; BIOPHYSICS; CELL LINE; CHEMISTRY; GENOMICS; METABOLISM; MUTATION; POSITION WEIGHT MATRIX; PROCEDURES; REGULATORY SEQUENCE; STATISTICAL MODEL;

EID: 84983740566     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv733     Document Type: Article
Times cited : (19)

References (47)
  • 1
    • 84925089678 scopus 로고    scopus 로고
    • The role of regulatory variation in complex traits and disease
    • Albert, F.W. and Kruglyak, L. (2015) The role of regulatory variation in complex traits and disease. Nat. Rev.Genet., 16, 197-212
    • (2015) Nat. Rev.Genet. , vol.16 , pp. 197-212
    • Albert, F.W.1    Kruglyak, L.2
  • 4
    • 84929308758 scopus 로고    scopus 로고
    • Current trend of annotating single nucleotide variation in humans-A case study on SNVrap
    • Li, M.J. and Wang, J. (2015) Current trend of annotating single nucleotide variation in humans-A case study on SNVrap. Methods, 79-80, 32-40
    • (2015) Methods , vol.79-80 , pp. 32-40
    • Li, M.J.1    Wang, J.2
  • 5
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar, P., Henikoff, S. and Ng, P.C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073-1081
    • (2009) Nat. Protoc. , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 7
    • 84881613239 scopus 로고    scopus 로고
    • DbNSFP v2.0: A database of human non-synonymous SNVs and their functional predictions and annotations
    • Liu, X., Jian, X. and Boerwinkle, E. (2013) dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat., 34, E2393-E2402
    • (2013) Hum. Mutat. , vol.34 , pp. E2393-E2402
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 8
    • 84908894973 scopus 로고    scopus 로고
    • Genome-wide analysis of noncoding regulatory mutations in cancer
    • Weinhold, N., Jacobsen, A., Schultz, N., Sander, C. and Lee, W. (2014) Genome-wide analysis of noncoding regulatory mutations in cancer Nat. Genet., 46, 1160-1165
    • (2014) Nat. Genet. , vol.46 , pp. 1160-1165
    • Weinhold, N.1    Jacobsen, A.2    Schultz, N.3    Sander, C.4    Lee, W.5
  • 10
    • 84922527340 scopus 로고    scopus 로고
    • Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types
    • Fredriksson, N.J., Ny, L., Nilsson, J.A. and Larsson, E. (2014) Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types. Nat. Genet., 46, 1258-1263
    • (2014) Nat. Genet. , vol.46 , pp. 1258-1263
    • Fredriksson, N.J.1    Ny, L.2    Nilsson, J.A.3    Larsson, E.4
  • 13
    • 23244456864 scopus 로고    scopus 로고
    • Identification of functional genetic variants in cyclooxygenase-2 and their association with risk of esophageal cancer
    • Zhang, X., Miao, X., Tan, W., Ning, B., Liu, Z., Hong, Y., Song, W., Guo, Y., Zhang, X., Shen, Y. et al. (2005) Identification of functional genetic variants in cyclooxygenase-2 and their association with risk of esophageal cancer. Gastroenterology, 129, 565-576
    • (2005) Gastroenterology , vol.129 , pp. 565-576
    • Zhang, X.1    Miao, X.2    Tan, W.3    Ning, B.4    Liu, Z.5    Hong, Y.6    Song, W.7    Guo, Y.8    Zhang, X.9    Shen, Y.10
  • 14
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura, M. (1968) Evolutionary rate at the molecular level. Nature, 217, 624-626
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 15
    • 84898985349 scopus 로고    scopus 로고
    • Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
    • Kheradpour, P. and Kellis, M. (2013) Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res., 42, 2976-2987
    • (2013) Nucleic Acids Res. , vol.42 , pp. 2976-2987
    • Kheradpour, P.1    Kellis, M.2
  • 17
    • 77950404192 scopus 로고    scopus 로고
    • Quantifying the effect of sequence variation on regulatory interactions
    • Manke, T., Heinig, M. and Vingron, M. (2010) Quantifying the effect of sequence variation on regulatory interactions. Hum. Mutat., 31, 477-483
    • (2010) Hum. Mutat. , vol.31 , pp. 477-483
    • Manke, T.1    Heinig, M.2    Vingron, M.3
  • 18
    • 77956513142 scopus 로고    scopus 로고
    • Is-rSNP: A novel technique for in silico regulatory SNP detection
    • 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
    • (2010) Bioinformatics , vol.26 , pp. i524-i530
    • Macintyre, G.1    Bailey, J.2    Haviv, I.3    Kowalczyk, A.4
  • 19
    • 70349623314 scopus 로고    scopus 로고
    • Cis-regulatory mutations in human disease
    • Epstein, D.J. (2009) Cis-regulatory mutations in human disease. Brief Funct. Genomic. Proteomic., 8, 310-316
    • (2009) Brief Funct. Genomic. Proteomic. , vol.8 , pp. 310-316
    • Epstein, D.J.1
  • 20
    • 84964696143 scopus 로고    scopus 로고
    • FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer
    • Fu, Y., Liu, Z., Lou, S., Bedford, J., Mu, X., Yip, K.Y., Khurana, E. and Gerstein, M. (2014) FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biol., 15, 480-495
    • (2014) Genome Biol. , vol.15 , pp. 480-495
    • Fu, Y.1    Liu, Z.2    Lou, S.3    Bedford, J.4    Mu, X.5    Yip, K.Y.6    Khurana, E.7    Gerstein, M.8
  • 21
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M., Witten, D.M., Jain, P., O'Roak, B.J., Cooper, G.M. and Shendure, J. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet., 46, 310-315
    • (2014) Nat. Genet. , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6
  • 22
    • 84895510920 scopus 로고    scopus 로고
    • Functional annotation of noncoding sequence variants
    • Ritchie, G.R., Dunham, I., Zeggini, E. and Flicek, P. (2014) Functional annotation of noncoding sequence variants. Nat. Methods, 11, 294-296
    • (2014) Nat. Methods , vol.11 , pp. 294-296
    • Ritchie, G.R.1    Dunham, I.2    Zeggini, E.3    Flicek, P.4
  • 24
    • 84891837451 scopus 로고    scopus 로고
    • The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine
    • Stenson, P.D., Mort, M., Ball, E.V., Shaw, K., Phillips, A. and Cooper, D.N. (2014) The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet., 133, 1-9
    • (2014) Hum Genet. , vol.133 , pp. 1-9
    • Stenson, P.D.1    Mort, M.2    Ball, E.V.3    Shaw, K.4    Phillips, A.5    Cooper, D.N.6
  • 25
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender, E., Dietze, P., Karas, H. and Knuppel, R. (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241
    • (1996) Nucleic Acids Res. , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 26
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. and Lenhard, B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94
    • (2004) Nucleic Acids Res. , vol.32 , pp. D91-D94
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 27
    • 78651303899 scopus 로고    scopus 로고
    • UniPROBE, update 2011: Expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
    • Robasky, K. and Bulyk, M.L. (2011) UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions Nucleic Acids Res., 39, D124-D128
    • (2011) Nucleic Acids Res. , vol.39 , pp. D124-D128
    • Robasky, K.1    Bulyk, M.L.2
  • 32
    • 84884769487 scopus 로고    scopus 로고
    • In search of low-frequency and rare variants affecting complex traits
    • Panoutsopoulou, K., Tachmazidou, I. and Zeggini, E. (2013) In search of low-frequency and rare variants affecting complex traits. Hum Mol. Genet., 22, R16-R21
    • (2013) Hum Mol. Genet. , vol.22 , pp. R16-R21
    • Panoutsopoulou, K.1    Tachmazidou, I.2    Zeggini, E.3
  • 33
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using GERP++
    • Davydov, E.V., Goode, D.L., Sirota, M., Cooper, G.M., Sidow, A. and Batzoglou, S. (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput. Biol., 6, e1001025
    • (2010) PLoS Comput. Biol. , vol.6 , pp. e1001025
    • Davydov, E.V.1    Goode, D.L.2    Sirota, M.3    Cooper, G.M.4    Sidow, A.5    Batzoglou, S.6
  • 34
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • Djordjevic, M., Sengupta, A.M. and Shraiman, B.I. (2003) A biophysical approach to transcription factor binding site discovery Genome Res., 13, 2381-2390
    • (2003) Genome Res. , vol.13 , pp. 2381-2390
    • Djordjevic, M.1    Sengupta, A.M.2    Shraiman, B.I.3
  • 35
    • 70450265377 scopus 로고    scopus 로고
    • BayesPI - A new model to study protein-DNA interactions: A case study of condition-specific protein binding parameters for Yeast transcription factors
    • Wang, J. and Morigen. (2009) BayesPI-a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. BMC Bioinformatics, 10, 345-362
    • (2009) BMC Bioinformatics , vol.10 , pp. 345-362
    • Wang, J.1    Morigen2
  • 36
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    • Foat, B.C., Morozov, A.V. and Bussemaker, H.J. (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics, 22, e141-e149
    • (2006) Bioinformatics , vol.22 , pp. e141-e149
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 37
    • 84908138119 scopus 로고    scopus 로고
    • Quality versus accuracy: Result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence
    • Wang, J. (2014) Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence. BMC Bioinformatics, 15, 289-304
    • (2014) BMC Bioinformatics , vol.15 , pp. 289-304
    • Wang, J.1
  • 38
    • 77955120332 scopus 로고    scopus 로고
    • The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
    • Wang, J. (2010) The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. BMC Bioinformatics, 11, 412-422
    • (2010) BMC Bioinformatics , vol.11 , pp. 412-422
    • Wang, J.1
  • 39
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • Zhao, Y., Granas, D. and Stormo, G.D. (2009) Inferring binding energies from selected binding sites. PLoS Comput. Biol., 5, e1000590
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000590
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 40
    • 33846700587 scopus 로고    scopus 로고
    • Predicting transcription factor affinities to DNA from a biophysical model
    • Roider, H.G., Kanhere, A., Manke, T. and Vingron, M. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics, 23, 134-141
    • (2007) Bioinformatics , vol.23 , pp. 134-141
    • Roider, H.G.1    Kanhere, A.2    Manke, T.3    Vingron, M.4
  • 42
    • 84969221125 scopus 로고    scopus 로고
    • Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation
    • Wang, J., Malecka, A., Trøenand, G. and Delabie, J. (2015) Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation. BMC Genomics, 16(Suppl. 7), S12
    • (2015) BMC Genomics , vol.16 , pp. S12
    • Wang, J.1    Malecka, A.2    Trøenand, G.3    Delabie, J.4
  • 43
    • 84857156980 scopus 로고    scopus 로고
    • Robust rank aggregation for gene list integration and meta-analysis
    • Kolde, R., Laur, S., Adler, P. and Vilo, J. (2012) Robust rank aggregation for gene list integration and meta-analysis Bioinformatics, 28, 573-580
    • (2012) Bioinformatics , vol.28 , pp. 573-580
    • Kolde, R.1    Laur, S.2    Adler, P.3    Vilo, J.4
  • 44
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    Von Hippel, P.H.2
  • 46
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: Key considerations in genomic analyses
    • Sims, D., Sudbery, I., Ilott, N.E., Heger, A. and Ponting, C.P. (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev., 15, 121-132
    • (2014) Nat. Rev. , vol.15 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 47
    • 84907270779 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of gastric adenocarcinoma
    • The, Cancer Genome Atlas Research Network (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513, 202-209.
    • (2014) Nature , vol.513 , pp. 202-209
    • The, Cancer Genome Atlas Research Network,1


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