Comparative analysis of proteome and transcriptome variation in mouse

PLoS Genetics

Volumn 7, Issue 6, 2011, Pages

  Ghazalpour, Anatole ^a   Bennett, Brian ^a   Petyuk, Vladislav A ^b   Orozco, Luz ^a   Hagopian, Raffi ^a   Mungrue, Imran N ^a   Farber, Charles R ^c   Sinsheimer, Janet ^a   Kang, Hyun M ^d   Furlotte, Nicholas ^e   Park, Christopher C ^a   Wen, Ping Zi ^a   Brewer, Heather ^b   Weitz, Karl ^b   Camp II, David G ^b   Pan, Calvin ^a   Yordanova, Roumyana ^f   Neuhaus, Isaac ^f   Tilford, Charles ^f   Siemers, Nathan ^f   Gargalovic, Peter ^f   Eskin, Eleazar ^e   Kirchgessner, Todd ^f   Smith, Desmond J ^a   Smith, Richard D ^b   Lusis, Aldons J ^a,g   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF VIRGINIA   (United States)

^d UNIVERSITY OF MICHIGAN   (United States)

^e University of California   (United States)

^f BRISTOL MYERS SQUIBB   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FACTOR; GENE PRODUCT; LIPOPROTEIN; MESSENGER RNA; PEPTIDE; PROTEIN; PROTEOME; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; BASIC RESEARCH; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE FUNCTION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; HIGH THROUGHPUT SCREENING; INBRED STRAIN; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MALE; MASS SPECTROMETRY; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; OBESITY; PROTEIN ANALYSIS; PROTEIN PROCESSING; ALTERNATIVE RNA SPLICING; ANIMAL; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; METABOLISM; PROTEOMICS;

MAMMALIA; MUS;

ALTERNATIVE SPLICING; ANIMALS; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; MICE; PROTEOME; PROTEOMICS; RNA, MESSENGER;

EID: 79959812980     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001393     Document Type: Article

References (46)

1. Brem RB, Yvert G, Clinton R, Kruglyak L, (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
2. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, et al. (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet 37: 225-232.
3. Ghazalpour A, Doss S, Kang H, Farber C, Wen PZ, et al. (2008) High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet 4: e1000149 doi:10.1371/journal.pgen.1000149.
4. Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, et al. (2006) Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet 2: e130 doi:10.1371/journal.pgen.0020130.
5. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, et al. (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 37: 243-253.
6. Jansen RC, Nap JP, (2001) Genetical genomics: the added value from segregation. Trends Genet 17: 388-391.
7. Keurentjes JJ, Fu J, Terpstra IR, Garcia JM, van den Ackerveken G, et al. (2007) Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 104: 1708-1713.
8. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
9. Vidal M, (2009) A unifying view of 21st century systems biology. FEBS Lett 583: 3891-3894.
10. Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, et al. (2007) Genetic basis of proteome variation in yeast. Nat Genet 39: 1369-1375.
11. Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, et al. (2009) System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet 41: 166-167.
12. Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, et al. (2010) A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 20: 281-290.
13. Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, et al. (2009) Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet 18: 4118-4129.
14. Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, et al. (2010) Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics 185: 1081-1095.
15. Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, et al. (2009) Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample. J Proteome Res 8: 290-299.
16. Ayroles JF, Carbone MA, Stone EA, Jordan KW, Lyman RF, et al. (2009) Systems genetics of complex traits in Drosophila melanogaster. Nat Genet 41: 299-307.
17. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC, (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30: e48.
18. Rogojina AT, Orr WE, Song BK, Geisert EE Jr, (2003) Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines. Mol Vis 9: 482-496.
19. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 5676-5684.
20. Zeisel A, Amir A, Kostler WJ, Domany E, (2010) Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. BMC Bioinformatics 11: 400.
21. Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, et al. (2004) A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 15: 276-284.
22. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
23. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
24. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
25. Fournier B, Saudubray JM, Benichou B, Lyonnet S, Munnich A, et al. (1994) Large deletion of the peroxisomal acyl-CoA oxidase gene in pseudoneonatal adrenoleukodystrophy. J Clin Invest 94: 526-531.
26. Walter NA, McWeeney SK, Peters ST, Belknap JK, Hitzemann R, et al. (2007) SNPs matter: impact on detection of differential expression. Nat Methods 4: 679-680.
27. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, et al. (2008) Efficient control of population structure in model organism association mapping. Genetics 178: 1709-1723.
28. Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, et al. (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448: 1050-1053.
29. Flint J, Valdar W, Shifman S, Mott R, (2005) Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev Genet 6: 271-286.
30. Bao L, Wei L, Peirce JL, Homayouni R, Li H, et al. (2006) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mamm Genome 17: 575-583.
31. Breitling R, Li Y, Tesson BM, Fu J, Wu C, et al. (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genet 4: e1000232 doi:10.1371/journal.pgen.1000232.
32. Park CC, Ahn S, Bloom JS, Lin A, Wang RT, et al. (2008) Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids. Nat Genet 40: 421-429.
33. van Nas A, Ingram-Drake L, Sinsheimer JS, Wang SS, Schadt EE, et al. (2010) Expression quantitative trait loci: replication, tissue- and sex-specificity in mice. Genetics 185: 1059-1068.
34. Calvo SE, Pagliarini DJ, Mootha VK, (2009) Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A 106: 7507-7512.
35. Mehrabian M, Qiao JH, Hyman R, Ruddle D, Laughton C, et al. (1993) Influence of the apoA-II gene locus on HDL levels and fatty streak development in mice. Arterioscler Thromb 13: 1-10.
36. Elias JE, Gygi SP, (2010) Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol 604: 55-71.
37. Petritis BO, Qian WJ, Camp DG 2nd, Smith RD, (2009) A simple procedure for effective quenching of trypsin activity and prevention of 18O-labeling back-exchange. J Proteome Res 8: 2157-2163.
38. Monroe ME, Tolic N, Jaitly N, Shaw JL, Adkins JN, et al. (2007) VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics 23: 2021-2023.
39. Zimmer JS, Monroe ME, Qian WJ, Smith RD, (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 25: 450-482.
40. Petyuk VA, Qian WJ, Smith RD, Smith DJ, (2010) Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry. Methods 50: 77-84.
41. Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, et al. (2009) Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinformatics 25: 2573-2580.
42. Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, et al. (2008) SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9: 313.
43. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
44. Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36: D724-728.
45. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
46. Langfelder P, Horvath S, (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559.