rSNP_Guide: An integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites

Human Mutation

Volumn 20, Issue 4, 2002, Pages 239-248

  Ponomarenko, Julia V ^a   Orlova, Galina V ^a   Merkulova, Tatyana I ^a   Gorshkova, Elena V ^a   Fokin, Oleg N ^a   Vasiliev, Gennady V ^a   Frolov, Anatoly S ^a   Ponomarenko, Mikhail P ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

Database; Disease susceptibility; DNA binding site; F9; HBG1; HPFH; HSPA1A; K ras; Mutation analysis; SNP; TDO2; Transcription factor

Indexed keywords

BLOOD CLOTTING FACTOR 9; GAMMA GLOBIN; GENE PRODUCT; HEAT SHOCK PROTEIN 70; K RAS PROTEIN; PROTEIN HBG1; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BIOINFORMATICS; DISEASE ASSOCIATION; DISEASE PREDISPOSITION; DNA BINDING; DNA SEQUENCE; GENE FUNCTION; GENE MUTATION; GENETIC ANALYSIS; GENOME; NUCLEOTIDE SEQUENCE; ONCOGENE K RAS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN BINDING; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS;

ANIMALS; BINDING SITES; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTRONS; MUTAGENESIS, SITE-DIRECTED; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS (GENETICS); RECEPTOR, ANGIOTENSIN, TYPE 1; RECEPTORS, ANGIOTENSIN; SOFTWARE; TRANSCRIPTION FACTORS; TRYPTOPHAN OXYGENASE;

EID: 0036390088     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.10116     Document Type: Article

References (39)

1. Beason KB, Acuff CG, Steinhelper ME, Elton TS. 1999. An A/T-rich cis-element is essential for rat angiotensin II type 1A receptor transcription in vascular smooth muscle cells. Biochim Biophys Acta 1444:25-34.
2. Bienvenu T, Lacronique V, Raymondjean M, Cazeneuve C, Hubert D, Kaplan J, Beldjord C. 1995. Three novel sequence variations in the 5′ upstream region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene: two polymorphisms and one putative molecular defect. Hum Genet 95:698-702.
3. Boccia LM, Lillicrap D, Newcombe K, Mueller CR. 1996. Binding of the Ets factor GA-binding protein to an upstream site in the factor 9 promoter is a critical event in transactivation. Mol Cell Biol 16:1929-1935.
4. Brookes A, Lehvaeslaiho H, Siegfried M, Boem J, Yuan Y, Sarkar C, Bork P, Ortigao E 2000. HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Res 28:356-360.
5. Chen B, Johanson L, Wiest J, Anderson M, You M. 1994. The second intron of the K-ras gene contains regulatory elements associated with mouse lung tumor susceptibility. Proc Natl Acad Sci USA 91:1589-1593.
6. Comings DE, Gade R, Muhleman D, Chiu C, Wu S, To M, Spence M, Dietz G, Winn-Deen E, Rosenthal RJ, Lesieur HR, Rugle L, Sverd J, Ferry L, Johnson JP, MacMurray JP. 1996. Exon and intron variants in the human tryptophan 2,3-dioxygenase gene: potential association with Tourette syndrome, substance abuse and other disorders. Pharmacogenetics 6:307-318.
7. Cowell JK, Bia B, Akoulitchev A. 1996. A novel mutation in the promotor region in a family with a mild form of retinoblastoma indicates the location of a new regulatory domain for the RB1 gene. Oncogene 12:431-436.
8. Crossley M, Brownlee GG. 1990. Disruption of a C/EBP binding site in the factor IX promoter is associated with haemophilia B. Nature. 345:444-446.
9. Gall J, Bellini M, Wu Z, Murphy C. 1999. Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes. Mol Biol Cell 10: 4385-4402.
10. Gillio AP, Verlander PC, Batish SD, Giampietro PF, Auerbach AD. 1997. Phenotypic consequences of mutations in the Fanconi anemia FAC gene: an international fanconi anemia registry study. Blood 90:105-110.
11. Hamosh A, Scott AF, Amberger J, Valle D, McKusick VA. 2000. Online Mendelian inheritance in man (OMIM). Hum Mutat 15:57-61.
12. Hirosawa S, Fahner JB, Salier JP, Wu CT, Lovrien EW, Kurachi K. 1990. Structural and functional basis of the developmental regulation of human coagulation factor IX gene: factor IX Leyden. Proc Natl Acad Sci USA 87: 4421-4425.
13. Knight JC, Udalova I, Hill AV, Greenwood BM, Peshu N, Marsh K, Kwiatkowski D. 1999. A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet 22:145-150.
14. Krawczak M, Ball E, Fenton I, Stenson PD, Abeysinghe S, Thomas N, Cooper DN. 2000. Human gene mutation database-a biomedical information and research resource. Hum Mutat 15:45-51.
15. Langdon S, Kaufman R. 1998. Gamma-globin gene promoter elements required for interaction with globin enhancers. Blood 91:309-318.
16. Mantovani R, Malgaretti N, Nicolis S, Ronchi A, Giglioni B, Ottolenghi S. 1988. The effects of HPFH mutations in the human gamma-globin promoter on binding of ubiquitous and erythroid specific nuclear factors. Nucleic Acids Res 16:7783-7797.
17. Marth G, Yeh R, Minton M, Donaldson R, Li Q, Duan S, Davenport R, Miller R, Kwok P-Y. 2001. Single-nucleotide polymorphisms in the public domain: how useful are they? Nat Genet 27:371-372.
18. Martin E, Nathan C, Xie QW. 1994. Role of interferon regulatory factor 1 in induction of nitric oxide synthase. J Exp Med 180:977-984.
19. Matsuda M, Sakamoto N, Fukumaki Y. 1992. Delta-thalassemia caused by disruption of the site for an erythroid-specific transcription factor, GATA-1, in the delta-globin gene promoter. Blood 80:1347-1351.
20. Moi P, Loudianos G, Lavinha J, Murru S, Cossu P, Casu R, Oggiano L, Longinotti M, Cao A, Pirastu M. 1992. Delta-thalassemia due to a mutation in an erythroid-specific binding protein sequence 3′ to the delta-globin gene. Blood 79:512-516.
21. Nedelcheva Kristensen V, Haraldsen EK, Anderson KB, Lonning PE, Erikstein B, Karesen R, Gabrielsen OS, Borresen-Dale AL. 1999. CYP17 and breast cancer risk: the polymorphism in the 5′ flanking area of the gene does not influence binding to Sp-1. Cancer Res 59:2825-2828.
22. O'Neill D, Kaysen J, Donovan-Peluso M, Castle M, Bank A. 1990. Protein-DNA interactions upstream from the human A gamma globin gene. Nucleic Acids Res 18:1977-1982.
23. Osier M, Cheung K-H, Kidd J, Pakstis A, Miller P, Kidd K. 2001. ALFRED: an allele frequency database for diverse populations and DNA polymorphisms: an update. Nucleic Acids Res 29:317-319.
24. Piedrafita FJ, Molander RB, Vansant G, Orlova EA, Pfahl M, Reynolds WE 1996. An Alu element in the myeloperoxidase promoter contains a composite SPl-thyroid hormoneretinoic acid response element. J Biol Chem 271:14412-14420.
25. Ponomarenko M, Ponomarenko J, Frolov A, Podkolodnaya O, Vorobyev DG, Kolchanov NA, Overton GC. 1999. Oligonucleotide frequency matrices addressed to recognizing functional DNA signals. Bioinformatics 15:631-643.
26. Ponomarenko J, Furman D, Frolov A, Podkolodny N, Orlova G, Ponomarenko M, Kolchanov N, Sarai A. 2001a. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res 29:284-287.
27. Ponomarenko J, Merkulova T, Vasiliev G, Levashova Z, Orlova G, Lavryushev S, Fokin O, Ponomarenko M, Frolov A, Sarai A. 2001b. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and signal-directed mutations. Nucleic Acids Res 29:312-316.
28. Ponomarenko J, Merkulova T, Orlova G, Fokin O, Gorshkova E, Ponomarenko M. 2002a. Mining DNA sequences to predict sites which mutations cause genetic diseases. Knowledge-Based Systems 15:225-233.
29. Ponomarenko J, Orlova G, Frolov A, Gelfand M, Ponomarenko M. 2002b. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic Acids Res 30:195-199.
30. Quandt K, Frech K, Karas H, Wingender E, Werner T 1995. MatInd and MatInspector: new fast and sensitive tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 23:4878-4884.
31. Roulet E, Fisch I, Bucher P, Mermod N. 1998. Evaluation of computer tools for prediction of transcription factor binding sites on genomic DNA. In Silico Biol 1:21-28.
32. Roulet E, Bucher P, Schneider R, Wingender E, Dusserre Y, Werner T, Mermod N. 1999. Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J Mol Biol 297:833-848.
33. Ryan J, Barker P, Nesbitt M, Ruddle E 1987. KRAS2 as a genetic marker for lung tumor susceptibility in inbred mice. J Natl Cancer Inst 79:1351-1357.
34. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Atshuler D, The International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1,42 million single nucleotide polymorphisms. Nature 409:928-933.
35. Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308-311.
36. Stoeckert C Jr, Salas F, Brunk B, Overton C. 1999. EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res 27:200-203.
37. Tsutsumi-Ishii Y, Tadokoro K, Hanaoka F, Tsuchida N. 1995. Response of heat shock element within of human HSP70 promoter of mutated p53 genes. Cell Growth Differ 6:1-8.
38. Vasiliev G, Merkulov V, Kobzev V, Merkulova T, Ponomarenko M, Kolchanov N. 1999. Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding signal. FEBS Lett 462:85-88.
39. Wu H, Lozano G. 1994. NF-kappa B activation of p53. A potential mechanism for suppressing cell growth in response to stress. J Biol Chem 269:20067-20074.