Establishing and validating regulatory regions for variant annotation and expression analysis

BMC Genomics

Volumn 17, Issue , 2016, Pages

  Kaplun, Alexander ^a   Krull, Mathias ^a   Lakshman, Karthick ^a   Matys, Volker ^a   Lewicki, Birgit ^a   Hogan, Jennifer D ^a  

^a QIAGEN Bioinformatics   (United States)

Author keywords

Annotation; Promoter; Regulatory variants; Transcription factor binding; Transcription start site; TRANSFAC

Indexed keywords

TRANSCRIPTION FACTOR; PROTEIN BINDING;

ALGORITHM; ARTICLE; BINDING SITE; DISEASE ASSOCIATION; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOME; GENOMICS; PREDICTION; PROMOTER REGION; PROTEIN BINDING; TRANSCRIPTION INITIATION SITE; VALIDATION STUDY; BIOLOGY; DNA SEQUENCE; GENE EXPRESSION; GENETIC VARIATION; HUMAN; METABOLISM; MOLECULAR GENETICS; MUTATION; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION; GENETIC VARIATION; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MUTATION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84978115932     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2724-0     Document Type: Article

References (23)

1. Ohno S. So much "junk" DNA in our genome. In: Smith HH, editor. Evolution of Genetic Systems. New York: Gordon and Breach; 1972. p. 366-70.
2. Sauna ZE, Kimchi-Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet. 2011;12:683-91.
3. Supek F, Minana B, Valcarcel J, Gabaldon T, Lehner B. Synonymous mutations frequently act as driver mutations in human cancers. Cell. 2014;156:1324-35.
4. Hunt RC, Simhadri VL, Iandoli M, Sauna ZE, Kimchi-Sarfaty C. Exposing synonymous mutations. Trends Genet. 2014;30:308-21.
5. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genet. 2014;133:1-9.
6. Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2009;37:D793-796.
7. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980-985.
8. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39:D945-50.
9. The Cancer Genome Atlas. 2005. http://cancergenome.nih.gov/.
10. Thorn C, Klein T, Altman R. PharmGKB: The Pharmacogenomics Knowledge Base. In: Innocenti F, van Schaik RHN, editors. Pharmacogenomics. Clifton, New Jersey: Methods and Protocols Humana Press; 2013. p. 311-320.
11. Kaplun A, Hogan JD, Schacherer F, Peter AP, Krishna S, Braun BR, et al. PGMD: a comprehensive manually curated pharmacogenomic database. Pharmacogenomics J. 2016;16:124-8.
12. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006;34:D108-110.
13. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-81.
14. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-9.
15. Kel A, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis O, Wingender E. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003;31:3576-9.
16. Classen CF, Riehmer V, Landwehr C, Kosfeld A, Heilmann S, Scholz C, et al. Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis. Hum Genet. 2013;132:825-41.
17. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensemble 2015. Nucleic Acids Res. 2015;43:D662-9.
18. ENCODE: Encyclopedia of DNA Elements. https://www.encodeproject.org/
19. Kabzińska D, Kotruchow K, Ryniewicz B, Kochański A. Two pathogenic mutations located within the 5'-regulatory sequence of the GJB1 gene affecting initiation of transcription and translation. Acta Biochim Pol. 2011;58:359-63.
20. Bondurand N, Girard M, Pingault V, Lemort N, Dubourg O, Goossens M. Human Connexin 32, a gap junction protein altered in the X-linked form of Charcot-Marie-Tooth disease, is directly regulated by the transcription factor SOX10. Hum Mol Genet. 2001;10:2783-95.
21. Tsai P-C, Chen C-H, Liu A-B, Chen Y-C, Soong B-W, Lin K-P, et al. Mutational analysis of the 5' non-coding region of GJB1 in a Taiwanese cohort with Charcot-Marie-Tooth neuropathy. J Neurol Sci. 2013;332:51-5.
22. Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, et al. Human gene-centered transcription factor networks for enhancers and disease variants. Cell. 2015;161:661-73.
23. Damjanovich K, Langa C, Blanco FJ, McDonald J, Botella LM, Bernabeu C, et al. 5'UTR mutations of ENG cause hereditary hemorrhagic telangiectasia. Orphanet J Rare Dis. 2011;6:85.