Identifying functional single nucleotide polymorphisms in the human CArGome

Physiological Genomics

Volumn 43, Issue 18, 2011, Pages 1038-1048

  Benson, Craig C ^a   Zhou, Qian ^b   Long, Xiaochun ^b   Miano, Joseph M ^b  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

Bioinformatics; Carg box; Serum response factor; Transcription factor binding site

Indexed keywords

DNA; LUCIFERASE; SERUM RESPONSE FACTOR; TRANSCRIPTION FACTOR;

ARTICLE; BIOINFORMATICS; DNA BINDING; GEL MOBILITY SHIFT ASSAY; GENE TARGETING; GENETIC ASSOCIATION; GENETIC SCREENING; HUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION FACTOR BINDING SITE;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENOME, HUMAN; HISTONES; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; SERUM RESPONSE FACTOR; TRANSCRIPTION INITIATION SITE;

EID: 80053153925     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00098.2011     Document Type: Article

References (90)

1. Ameur A, Rada-Iglesias A, Komorowski J, Wadelius C. Identification of candidate regulatory SNPs by combination of transcription-factorbinding site prediction, SNP genotyping and haploChIP. Nucleic Acids Res 37: e85, 2009.
2. Andersen MC, Engstrom PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol 4: e5, 2008.
3. Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res 38: e126, 2010.
4. Buchwalter G, Gross C, Wasylyk B. Ets ternary complex transcription factors. Gene 324: 1-14, 2004.
5. Buckland PR. The importance and identification of regulatory polymorphisms and their mechanisms of action. Biochim Biophys Acta 1762: 17-28, 2006.
6. Chang VK, Donato JJ, Chan CS, Tye BK. Mcm1 promotes replication initiation by binding specific elements at replication origins. Mol Cell Biol 24: 6514-6524, 2004.
7. Chelala C, Khan A, Lemoine NR. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 25: 655-661, 2009.
8. Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol 9: R170, 2008.
9. Chen X, Tompa M. Comparative assessment of methods for aligning multiple genome sequences. Nat Biotechnol 28: 567-572, 2010.
10. Chorley BN, Wang X, Campbell MR, Pittman GS, Noureddine MA, Bell DA. Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat Res 659: 147-157, 2008.
11. Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913, 2005.
12. Cooper SJ, Trinklein ND, Nguyen L, Myers RM. Serum response factor binding sites differ in three human cell types. Genome Res 17: 136-144, 2007.
13. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 14: 1188-1190, 2004.
14. Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 8, Suppl 7: S21, 2007.
15. Donnelly P. Progress and challenges in genome-wide association studies in humans. Nature 456: 728-731, 2008.
16. Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 16: 1455-1464, 2006.
17. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816, 2007.
18. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM. Ensembl 2011. Nucleic Acids Res 39: D800-D806, 2011.
19. Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 10: 241-251, 2009.
20. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ, Open Regulatory Annotation Consortium. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 36: D107-D113, 2008.
21. Guo Y, Jamison DC. The distribution of SNPs in human gene regulatory regions. BMC Genomics 6: 140, 2005.
22. Guryev V, Berezikov E, Cuppen E. CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. BMC Genomics 6: 10, 2005.
23. Han YJ, Hu WY, Chernaya O, Antic N, Gu L, Gupta M, Piano M, de Lanerolle P. Increased myosin light chain kinase expression in hypertension: Regulation by serum response factor via an insertion mutation in the promoter. Mol Biol Cell 17: 4039-4050, 2006.
24. Hannenhalli S. Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics 24: 1325-1331, 2008.
25. Hardy J, Singleton A. Genomewide association studies and human disease. N Engl J Med 360: 1759-1768, 2009.
26. Hautmann MB, Madsen CS, Mack CP, Owens GK. Substitution of the degenerate smooth muscle (SM) alpha-actin CC(A/T-rich)6GG elements with c-fos serum response elements results in increased basal expression but relaxed SM cell specificity and reduced angiotensin II inducibility. J Biol Chem 273: 8398-8406, 1998.
27. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106: 9362-9367, 2009.
28. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108, 2005.
29. Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW. oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res 35: W245-W252, 2007.
30. Hooghe B, Hulpiau P, van Roy F, De Bleser P. ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. Nucleic Acids Res 36: W128-W132, 2008.
31. Hudson TJ. Wanted: regulatory SNPs. Nat Genet 33: 439-440, 2003.
32. Johansen FE, Prywes R. Serum response factor: transcriptional regulation of genes induced by growth factors and differentiation. Biochim Biophys Acta 1242: 1-10, 1995.
33. Johnson AD, O'Donnell CJ. An open access database of genome-wide association results. BMC Med Genet 10: 6, 2009.
34. Joliot V, Demma M, Prywes R. Interaction with RAP74 subunit of TFIIF is required for transcriptional activation by serum response factor. Nature 373: 632-635, 1995.
35. Karchin R. Next generation tools for the annotation of human SNPs. Brief Bioinform 10: 35-52, 2009.
36. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. Variation in transcription factor binding among humans. Science 328: 232-235, 2010.
37. Kasza A, Wyrzykowska P, Horwacik I, Tymoszuk P, Mizgalska D, Palmer K, Rokita H, Sharrocks AD, Jura J. Transcription factors Elk-1 and SRF are engaged in IL1-dependent regulation of ZC3H12A expression. BMC Mol Biol 11: 14, 2010.
38. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 12: 996-1006, 2002.
39. Knight JC. Regulatory polymorphisms underlying complex disease traits. J Mol Med 83: 97-109, 2005.
40. Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT, Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics 27: 715-717, 2010.
41. Kuwahara K, Kinoshita H, Kuwabara Y, Nakagawa Y, Usami S, Minami T, Yamada Y, Fujiwara M, Nakao K. Myocardin-related transcription factor A is a common mediator of mechanical stress-and neurohumoral stimulation-induced cardiac hypertrophic signaling leading to activation of brain natriuretic peptide gene expression. Mol Cell Biol 30: 4134-4148, 2010.
42. Leung S, Miyamoto NG. Point mutational analysis of the human c-fos serum response factor binding site. Nucleic Acids Res 17: 1177-1195, 1989.
43. Long X, Tharp DL, Georger MA, Slivano OJ, Lee MY, Wamhoff BR, Bowles DK, Miano JM. The smooth muscle cell-restricted KCNMB1 ion channel subunit is a direct transcriptional target of serum response factor and myocardin. J Biol Chem 284: 33671-33682, 2009.
44. Macintyre G, Bailey J, Haviv I, Kowalczyk A. is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics 26: i524-30, 2010.
45. Manke T, Heinig M, Vingron M. Quantifying the effect of sequence variation on regulatory interactions. Hum Mutat 31: 477-483, 2010.
46. Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med 363: 166-176, 2010.
47. Martin MM, Buckenberger JA, Jiang J, Malana GE, Nuovo GJ, Chotani M, Feldman DS, Schmittgen TD, Elton TS. The human angiotensin II type 1 receptor +1166 A/C polymorphism attenuates microRNA-155 binding. J Biol Chem 282: 24262-24269, 2007.
48. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369, 2008.
49. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28: 495-501, 2010.
50. Miano JM. Role of serum response factor in the pathogenesis of disease. Lab Invest 90: 1274-1284, 2010.
51. Miano JM. Serum response factor: toggling between disparate programs of gene expression. J Mol Cell Cardiol 35: 577-593, 2003.
52. Miano JM, Carlson MJ, Spencer JA, Misra RP. Serum response factor-dependent regulation of the smooth muscle calponin gene. J Biol Chem 275: 9814-9822, 2000.
53. Miano JM, Long X, Fujiwara K. Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus. Am J Physiol Cell Physiol 292: C70-C81, 2007.
54. Mokalled MH, Johnson A, Kim Y, Oh J, Olson EN. Myocardin-related transcription factors regulate the Cdk5/Pctaire1 kinase cascade to control neurite outgrowth, neuronal migration and brain development. Development 137: 2365-2374, 2010.
55. Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, Li X, Li H, Kuperwasser N, Ruda VM, Pirruccello JP, Muchmore B, Prokunina-Olsson L, Hall JL, Schadt EE, Morales CR, Lund-Katz S, Phillips MC, Wong J, Cantley W, Racie T, Ejebe KG, Orho-Melander M, Melander O, Koteliansky V, Fitzgerald K, Krauss RM, Cowan CA, Kathiresan S, Rader DJ. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466: 714-719, 2010.
56. Niu Z, Li A, Zhang SX, Schwartz RJ. Serum response factor micromanaging cardiogenesis. Curr Opin Cell Biol 19: 618-627, 2007.
57. Pampin S, Rodriguez-Rey JC. Functional analysis of regulatory singlenucleotide polymorphisms. Curr Opin Lipidol 18: 194-198, 2007.
58. Park C, Hennig GW, Sanders KM, Cho JH, Hatton WJ, Redelman D, Park JK, Ward SM, Miano JM, Yan W, Ro S. SRF-dependent microRNAs regulate gastrointestinal smooth muscle cell phenotypes. Gastroenterology 141: 164-175, 2011.
59. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680, 2009.
60. Philippar U, Schratt G, Dieterich C, Muller JM, Galgoczy P, Engel FB, Keating MT, Gertler F, Schule R, Vingron M, Nordheim A. The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF. Mol Cell 16: 867-880, 2004.
61. Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M. SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res 37: D803-D809, 2009.
62. Pollock R, Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res 18: 6197-6204, 1990.
63. Ponomarenko JV, Merkulova TI, Orlova GV, Fokin ON, Gorshkova EV, Frolov AS, Valuev VP, Ponomarenko MP. rSNP Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. Nucleic Acids Res 31: 118-121, 2003.
64. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38: D105-D110, 2010.
65. Prokunina L, Alarcon-Riquelme ME. Regulatory SNPs in complex diseases: their identification and functional validation. Expert Rev Mol Med 6: 1-15, 2004.
66. Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res 39: D871-D875, 2011.
67. Rebbeck TR, Spitz M, Wu X. Assessing the function of genetic variants in candidate gene association studies. Nat Rev Genet 5: 589-597, 2004.
68. Sandelin A. Prediction of regulatory elements. Methods Mol Biol 453: 233-244, 2008.
69. Selvaraj A, Prywes R. Expression profiling of serum inducible genes identifies a subset of SRF target genes that are MKL dependent. BMC Mol Biol 5: 13, 2004.
70. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311, 2001.
71. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050, 2005.
72. Stepanek J, Vincent M, Turpin PY, Paulin D, Fermandjian S, Alpert B, Zentz C. C->G base mutations in the CArG box of c-fos serum response element alter its bending flexibility: consequences for core-SRF recognition. FEBS J 274: 2333-2348, 2007.
73. Sullivan AL, Benner C, Heinz S, Huang W, Xie L, Miano JM, Glass CK. Serum response factor utilizes distinct promoter-and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages. Mol Cell Biol 31: 861-875, 2011.
74. Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ. SNPs in human miRNA genes affect biogenesis and function. RNA 15: 1640-1651, 2009.
75. Sun Q, Chen G, Streb JW, Long X, Yang Y, Stoeckert CJ Jr, Miano JM. Defining the mammalian CArGome. Genome Res 16: 197-207, 2006.
76. Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet 81: 829-834, 2007.
77. Tokovenko B, Golda R, Protas O, Obolenskaya M, El'skaya A. COTRASIF: conservation-aided transcription-factor-binding site finder. Nucleic Acids Res 37: e49, 2009.
78. Torkamani A, Schork NJ. Predicting functional regulatory polymorphisms. Bioinformatics 24: 1787-1792, 2008.
79. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM. An abundance of bidirectional promoters in the human genome. Genome Res 14: 62-66, 2004.
80. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Meth 5: 829-834, 2008.
81. Wang X, Tomso DJ, Chorley BN, Cho HY, Cheung VG, Kleeberger SR, Bell DA. Identification of polymorphic antioxidant response elements in the human genome. Hum Mol Genet 16: 1188-1200, 2007.
82. Ward LD, Bussemaker HJ. Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 24: i165-71, 2008.
83. Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5: 276-287, 2004.
84. Won KJ, Ren B, Wang W. Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol 11: R7, 2010.
85. Woo YH, Walker M, Churchill GA. Coordinated expression domains in mammalian genomes. PLoS One 5: e12158, 2010.
86. Xie X, Rigor P, Baldi P. MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 25: 167-174, 2009.
87. Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res 37: W600-W605, 2009.
88. Zhang SX, Garcia-Gras E, Wycuff DR, Marriot SJ, Kadeer N, Yu W, Olson EN, Garry DJ, Parmacek MS, Schwartz RJ. Identification of direct serum-response factor gene targets during Me2SO-induced P19 cardiac cell differentiation. J Biol Chem 280: 19115-19126, 2005.
89. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci USA 102: 4459-4464, 2005.
90. Zhao Y, Samal E, Srivastava D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220, 2005.