Genomics meets proteomics: Identifying the culprits in disease

Human Genetics

Volumn 133, Issue 6, 2014, Pages 689-700

  Stunnenberg, Hendrik G ^a   Hubner, Nina C ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; PROTEIN; RNA; TRANSCRIPTION FACTOR;

BREAST CANCER; CANCER RISK; CHROMATIN; EPIGENETICS; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC RISK; GENOMICS; HUMAN; HUMAN GENOME; MASS SPECTROMETRY; PERSONALIZED MEDICINE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE TRAIT LOCUS; REVIEW; RISK REDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMATIN; EPIGENESIS, GENETIC; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDIVIDUALIZED MEDICINE; PROTEOME; TANDEM MASS SPECTROMETRY;

EID: 84901034831     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1376-2     Document Type: Review

References (103)

1. A Catalog of Published Genome-Wide Association Studies (2013). http://www.genome.gov/gwastudies. Accessed 11 May 2013
2. Adams D, Altucci L, Antonarakis S, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis E, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, Lernmark Å, Leslie D, Loeffler M, Macintyre E, Mai A, Martens J, Minucci S, Ouwehand W, Pelicci P, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg H, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol 30(3):224-226
3. Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R (2010) Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol 11(11):789-801
4. Altmuller J, Palmer LJ, Fischer G, Scherb H, Wjst M (2001) Genomewide scans of complex human diseases: true linkage is hard to find. Am J Hum Genet 69(5):936-950
5. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Bonnen PE, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Gonzaga-Jauregui C, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58
6. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324(5935):1720-1723
7. Bartels SJ, Spruijt CG, Brinkman AB, Jansen PW, Vermeulen M, Stunnenberg HG (2011) A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein. PLoS ONE 6(10):e25884
8. Bell J, Pai A, Pickrell J, Gaffney D, Pique-Regi R, Degner J, Gilad Y, Pritchard J (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 12(1)
9. Boersema P, Raijmakers R, Lemeer S, Mohammed S, Heck A (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 4(4):484-494
10. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228-237
11. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132(2):311-322
12. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 22(9):1790-1797
13. Brem RB, Storey JD, Whittle J, Kruglyak L (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436(7051):701-703
14. Butter F, Kappei D, Buchholz F, Vermeulen M, Mann M (2010) A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth. EMBO Rep 11(4):305-311
15. Butter F, Davison L, Viturawong T, Scheibe M, Vermeulen M, Todd JA, Mann M (2012) Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet 8(9):e1002982
16. Byrum SD, Raman A, Taverna SD, Tackett AJ (2012) ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep 2(1):198-205
17. Califano A, Butte AJ, Friend S, Ideker T, Schadt E (2012) Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet 44(8):841-847
18. Chadwick LH (2012) The NIH Roadmap Epigenomics Program data resource. Epigenomics 4(3):317-324
19. Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11(6):427-439
20. Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10(3):184-194
21. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16(1):123-131
22. Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292-301
23. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, Langerod A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Borresen-Dale AL, Brenton JD, Tavare S, Caldas C, Aparicio S (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486(7403):346-352
24. Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczynska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Sillje HH, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA (2013) SMIM1 underlies the Vel blood group and influences red blood cell traits. Nat Genet 45(5):542-545
25. de Godoy L, Olsen J, Cox J, Nielsen M, Hubner N, Fröhlich F, Walther T, Mann M (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455(7217):1251-1254
26. de Wit E, de Laat W (2012) A decade of 3C technologies: insights into nuclear organization. Genes Dev 26(1):11-24
27. Dejardin J, Kingston RE (2009) Purification of proteins associated with specific genomic loci. Cell 136(1):175-186
28. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, Gagnebin M, Nisbett J, Deloukas P, Dermitzakis ET, Antonarakis SE (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325(5945):1246-1250
29. Dixon J, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu J, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376-380
30. Easton A, Webster LA, Eacott MJ (2012) The episodic nature of episodic-like memories. Learn Mem 19(4):146-150
31. Elefsinioti A, Sarac OS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A (2011) Large-scale de novo prediction of physical protein-protein association. Mol Cell Proteomics 10(11):M111 010629
32. Ernst J, Kheradpour P, Mikkelsen T, Shoresh N, Ward L, Epstein C, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein B (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43-49
33. Everley RA, Kunz RC, McAllister FE, Gygi SP (2013) Increasing throughput in targeted proteomics assays: 54-plex Quantitation in a single mass spectrometry run. Anal Chem
34. Foss E, Radulovic D, Shaffer S, Ruderfer D, Bedalov A, Goodlett D, Kruglyak L (2007) Genetic basis of proteome variation in yeast. Nat Genet 39(11):1369-1375
35. Freedman M, Monteiro A, Gayther S, Coetzee G, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D, James M, Liu P, Tichelaar J, Vikis H, You M, Mills I (2011) Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 43(6):513-518
36. Fried M, Crothers DM (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9(23):6505-6525
37. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58-64
38. Garner MM, Revzin A (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 9(13):3047-3060
39. Genomes Project Consortium, Abecasis G, Auton A, Brooks L, DePristo M, Durbin R, Handsaker R, Kang H, Marth G, McVean G (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65
40. Gibbs J, van der Brug M, Hernandez D, Traynor B, Nalls M, Lai S-L, Arepalli S, Dillman A, Rafferty I, Troncoso J, Johnson R, Zielke H, Ferrucci L, Longo D, Cookson M, Singleton A (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6(5)
41. Gibson G (2011) Rare and common variants: twenty arguments. Nat Rev Genet 13(2):135-145
42. Gibson PR, Shepherd SJ (2012) Food choice as a key management strategy for functional gastrointestinal symptoms. Am J Gastroenterol 107(5):657-666; quiz 667
43. Glatter T, Wepf A, Aebersold R, Gstaiger M (2009) An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol 5
44. Grossman S, Andersen K, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park D, Griesemer D, Karlsson E, Wong S, Cabili M, Adegbola R, Bamezai R, Hill A, Vannberg F, Rinn J, Genomes P, Lander E, Schaffner S, Sabeti P (2013) Identifying recent adaptations in large-scale genomic data. Cell 152(4):703-713
45. Gygi S, Rist B, Gerber S, Turecek F, Gelb M, Aebersold R (1999a) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994-999
46. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999b) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19(3):1720-1730
47. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA (2011) 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response. Nature 470(7333):264-268
48. Hebert AS, Merrill AE, Bailey DJ, Still AJ, Westphall MS, Strieter ER, Pagliarini DJ, Coon JJ (2013) Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Methods 10(4):332-334
49. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243):108-112
50. Hesselberth J, Chen X, Zhang Z, Sabo P, Sandstrom R, Reynolds A, Thurman R, Neph S, Kuehn M, Noble W, Fields S, Stamatoyannopoulos J (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283-289
51. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis G (2012) Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 44(8):955-959
52. Hubner N, Mann M (2011) Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). Methods (San Diego, Calif) 53(4):453-459
53. Hubner N, Bird A, Cox J, Splettstoesser B, Bandilla P, Poser I, Hyman A, Mann M (2010) Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 189(4):739-754
54. Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, Yan C, Khalid O, Kantoff P, Oh W, Manak J, Berman B, Henderson B, Frenkel B, Haiman C, Freedman M, Tanay A, Coetzee G (2009) Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet 5(8)
55. Johnson CP, Tang HY, Carag C, Speicher DW, Discher DE (2007) Forced unfolding of proteins within cells. Science 317(5838):663-666
56. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J (2013) DNA-binding specificities of human transcription factors. Cell 152(1-2):327-339
57. 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 (2010) Variation in transcription factor binding among humans. Science 328(5975):232-235
58. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308(5720):385-389
59. Kristensen AR, Gsponer J, Foster LJ (2012) A high-throughput approach for measuring temporal changes in the interactome. Nat Methods 9(9):907-909
60. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25(3):309-316
61. Leinonen R, Sugawara H, Shumway M (2011) The sequence read archive. Nucleic Acids Res 39(Database issue):D19-D21
62. Li G, Ruan X, Auerbach R, Sandhu K, Zheng M, Wang P, Poh H, Goh Y, Lim J, Zhang J, Sim H, Peh S, Mulawadi F, Ong C, Orlov Y, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei C-L, Ge W, Wang H, Davis C, Fisher-Aylor K, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood M, Cheung E, Liu E, Sung W-K, Snyder M, Ruan Y (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148(1-2):84-98
63. Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML (2013) Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell 152(3):633-641
64. Manolio TA, Bailey-Wilson JE, Collins FS (2006) Genes, environment and the value of prospective cohort studies. Nat Rev Genet 7(10):812-820
65. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337(6099):1190-1195
66. Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI (2013) The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 10(8):730-736
67. Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J (2013) Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci USA 110(9):3645-3650
68. Mittler G, Butter F, Mann M (2009) A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res 19(2):284-293
69. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ (2011) The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol 7:550
70. Nejentsev S, Walker N, Riches D, Egholm M, Todd J (2009) Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science (New York, NY) 324(5925):387-389
71. Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31(13):3812-3814
72. Nikolov M, Schmidt C, Urlaub H (2012) Quantitative mass spectrometry-based proteomics: an overview. Methods Mol Biol 893:85-100
73. Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133(7):1277-1289
74. Ong S-E, Blagoev B, Kratchmarova I, Kristensen D, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376-386
75. Paul DS, Nisbet JP, Yang TP, Meacham S, Rendon A, Hautaviita K, Tallila J, White J, Tijssen MR, Sivapalaratnam S, Basart H, Trip MD, Gottgens B, Soranzo N, Ouwehand WH, Deloukas P (2011) Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits. PLoS Genet 7(6):e1002139
76. Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138(4):795-806
77. Picotti P, Clement-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Rost H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R (2013) A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 494(7436):266-270
78. Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J, Aebersold R (2003) The study of macromolecular complexes by quantitative proteomics. Nat Genet 33(3):349-355
79. Raval A, Tanner SM, Byrd JC, Angerman EB, Perko JD, Chen SS, Hackanson B, Grever MR, Lucas DM, Matkovic JJ, Lin TS, Kipps TJ, Murray F, Weisenburger D, Sanger W, Lynch J, Watson P, Jansen M, Yoshinaga Y, Rosenquist R, de Jong PJ, Coggill P, Beck S, Lynch H, de la Chapelle A, Plass C (2007) Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell 129(5):879-890
80. Reddy T, Gertz J, Pauli F, Kucera K, Varley K, Newberry K, Marinov G, Mortazavi A, Williams B, Song L, Crawford G, Wold B, Willard H, Myers R (2012) Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res 22(5):860-869
81. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273(5281):1516-1517
82. Rivas M, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang C, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn J, Kuruvilla F, Lagacé C, Neale B, Lo K, Schumm P, Törkvist L, National Institute of Diabetes, Digestive Kidney Diseases Inflammatory Bowel Disease Genetics C, United Kingdom Inflammatory Bowel Disease Genetics Consortium, International Inflammatory Bowel Disease Genetics Consortium, Dubinsky M, Brant S, Silverberg M, Duerr R, Altshuler D, Gabriel S, Lettre G, Franke A, D'Amato M, McGovern D, Cho J, Rioux J, Xavier R, Daly M (2011) Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 43(11):1066-1073
83. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4(8):651-657
84. Ross P, Huang Y, Marchese J, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin D (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154-1169
85. Saccone SF, Quan J, Mehta G, Bolze R, Thomas P, Deelman E, Tischfield JA, Rice JP (2011) New tools and methods for direct programmatic access to the dbSNP relational database. Nucleic Acids Res 39(Database issue):D901-D907
86. Saeed S, Logie C, Francoijs KJ, Frige G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG (2012) Chromatin accessibility, p300, and histone acetylation define PML-RARalpha and AML1-ETO binding sites in acute myeloid leukemia. Blood 120(15):3058-3068
87. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M (2012a) Linking disease associations with regulatory information in the human genome. Genome Res 22(9):1748-1759
88. Schaub RE, Poole SJ, Garza-Sanchez F, Benbow S, Hayes CS (2012b) Proteobacterial ArfA peptides are synthesized from non-stop messenger RNAs. J Biol Chem 287(35):29765-29775
89. Scheibe M, Butter F, Hafner M, Tuschl T, Mann M (2012) Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res 40(19):9897-9902
90. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473(7347):337-342
91. Slatkin M (2008) Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9(6):477-485
92. Smith LT, Lin M, Brena RM, Lang JC, Schuller DE, Otterson GA, Morrison CD, Smiraglia DJ, Plass C (2006) Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer. Proc Natl Acad Sci USA 103(4):982-987
93. Sowa ME, Bennett EJ, Gygi SP, Harper JW (2009) Defining the human deubiquitinating enzyme interaction landscape. Cell 138(2):389-403
94. Spruijt C, Gnerlich F, Smits A, Pfaffeneder T, Jansen P, Bauer C, Münzel M, Wagner M, Müller M, Khan F, Eberl H, Mensinga A, Brinkman A, Lephikov K, Müller U, Walter J, Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M (2013) Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152(5):1146-1159
95. Stunnenberg HG, Vermeulen M (2011) Towards cracking the epigenetic code using a combination of high-throughput epigenomics and quantitative mass spectrometry-based proteomics. BioEssays 33(7):547-551
96. Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed A, Hamon C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75(8):1895-1904
97. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabasi AL, Vidal M (2009) An empirical framework for binary interactome mapping. Nat Methods 6(1):83-90
98. Vermeulen M, Hubner N, Mann M (2008) High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Curr Opin Biotechnol 19(4):331-337
99. Visel A, Rubin EM, Pennacchio LA (2009) Genomic views of distant-acting enhancers. Nature 461(7261):199-205
100. Visscher PM (2008) Sizing up human height variation. Nat Genet 40(5):489-490
101. Wisniewski JR, Dus K, Mann M (2013) Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins. Proteomics Clin Appl 7(3-4):225-233
102. Wu L, Candille SI, Choi Y, Xie D, Jiang L, Li-Pook-Than J, Tang H, Snyder M (2013) Variation and genetic control of protein abundance in humans. Nature
103. Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M (2012) A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics 11(3):O111 009613