Identification of Functional cis-regulatory Polymorphisms in the Human Genome

Human Mutation

Volumn 34, Issue 5, 2013, Pages 735-742

  Molineris, Ivan ^a   Schiavone, Davide ^a,d   Rosa, Fabio ^b   Matullo, Giuseppe ^a,b   Poli, Valeria ^a   Provero, Paolo ^a,c  

^a UNIVERSITY OF TURIN   (Italy)

^b Human Genetics Foundation   (Italy)

^c SAN RAFFAELE HOSPITAL   (Italy)

^d MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Gene expression; Gene regulation; Polymorphisms; Transcription factors

Indexed keywords

INTERLEUKIN 6; STAT3 PROTEIN;

ARTICLE; COMPUTER ANALYSIS; DNA POLYMORPHISM; GENE INDUCTION; GENETIC ALGORITHM; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; INTRON; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; REGULATORY DNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CELL LINE; DATABASES, PROTEIN; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; REGULATORY SEQUENCES, NUCLEIC ACID; STAT3 TRANSCRIPTION FACTOR;

EID: 84876323005     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22299     Document Type: Article

References (22)

1. 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
2. Alenina N, Bashammakh S, Bader M. 2006. Specification and differentiation of serotonergic neurons. Stem Cell Rev 2(1):5-10.
3. Ameur A, Rada-Iglesias A, Komorowski J, Wadelius C. 2009. Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. Nucleic Acids Res 37(12):e85.
4. Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. 2008. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol 4(1):e5.
5. Armitage P. 1955. Tests for linear trends in proportions and frequencies. Biometrics 11(3):375-386.
6. Bai RK, Wong LJC. 2004. Detection and quantification of heteroplasmic mutant mitochondrial DNA by real-time amplification refractory mutation system quantitative PCR analysis: a single-step approach. Clin Chem 50(6):996-1001.
7. Balding DJ. 2006. A tutorial on statistical methods for population association studies. Nat Rev Genet 7(10):781-791.
8. Clay HB, Sillivan S, Konradi C. 2011. Mitochondrial dysfunction and pathology in bipolar disorder and schizophrenia. Int J Dev Neurosci 29(3):311-324.
9. Consortium WTCC. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447(7145):661-678.
10. Epstein DJ. 2009. Cis-regulatory mutations in human disease. Brief Funct Genomics Proteomic 8(4):310-316.
11. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43-49.
12. Kaneto H, Matsuoka Ta, Miyatsuka T, Kawamori D, Katakami N, Yamasaki Y, Matsuhisa M. 2008. PDX-1 functions as a master factor in the pancreas. Front Biosci 13:6406-6420.
13. Lapidot M, Michal L, Mizrahi-Man O, Pilpel Y. 2008. Functional characterization of variations on regulatory motifs. PLoS Genet 4(3):e1000018.
14. Lappalainen T, Dermitzakis ET. 2010. Evolutionary history of regulatory variation in human populations. Hum Mol Genet 19(R2):R197-R203.
15. Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9(4):e1001046.
16. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17(7):2503-2516.
17. Poli V, Alonzi T. 2003. STAT3 function in vivo. In: Sehgal P, Levy D, Hirano T, editors. Signal transducers and activators of transcription (STATs): activation. Dordrecht, The Netherlands: Kluwer, p 493-512.
18. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315(5813):848-853.
19. Vallania F, Schiavone D, Dewilde S, Pupo E, Garbay S, Calogero R, Pontoglio M, Provero P, Poli V. 2009. Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3. Proc Natl Acad Sci USA 106(13):5117-5122.
20. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. 2009. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10(4):252-263.
21. Viken MK, Blomhoff A, Olsson M, Akselsen HE, Pociot F, Nerup J, Kockum I, Cambon-Thomsen A, Thorsby E, Undlien DE, Lie BA. 2009. Reproducible association with type 1 diabetes in the extended class I region of the major histocompatibility complex. Genes Immun 10(4):323-333.
22. Wang Y, Joseph SJ, Liu X, Kelly M, Rekaya R. 2011. SNPxGE2: a database for human SNP-coexpression associations. Bioinformatics 28(3):403-410.