Skip to main content
SpringerLink
Log in

Systems genetics, bioinformatics and eQTL mapping

  • Review
  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Jansen and Nap (Trends Genet 17(7):388–391, 2001) and Jansen (Nat Rev Genet 4:145–151, 2003) first proposed the concept of genetical genomics, or genome-wide genetic analysis of gene expression data, which is also called transcriptome mapping. In this approach, microarrays are used for measuring gene expression levels across genetic mapping populations. These gene expression patterns have been used for genome-wide association analysis, an analysis referred to as expression QTL (eQTL) mapping. Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. Bioinformatics is essential to genome-wide analysis of gene expression data and used as an effective tool for eQTL mapping. The use of Plabsoft database, EcoTILLING, GNARE and FastMap allowed for dramatic reduction of time in genome analysis. Some web-based tools (e.g., Lirnet, eQTL Viewer) provide efficient and intuitive ways for biologists to explore transcriptional regulation patterns, and to generate hypotheses on the genetic basis of transcriptional regulations. Expression quantitative trait loci (eQTL) mapping concerns finding genomic variation to elucidate variation of expression traits. This problem poses significant challenges due to high dimensionality of both the gene expression and the genomic marker data. The core challenges in understanding and explaining eQTL associations are the fine mapping and the lack of mechanistic explanation. But with the development of genetical genomics and computer technology, many new approaches for eQTL mapping will emerge. The statistical methods used for the analysis of expression QTL will become mature in the future.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Abraham AP, Miguel V, Rathi S, Helen MK, Cheryl LR, Li Na, Sue BK, Carrie SM, John KB, Conrad TG, Tamara JP (2005) Gene expression differences in mice divergently selected for methamphetamine sensitivity. Mamm Genome 16:291–305. doi:10.1007/s00335-004-2451-8

    Article  Google Scholar 

  • Adam R, Fernando PMV, Wang W, Leonard M, David WT (2007) The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. Mamm Genome 18:473–481. doi:10.1007/s00335-007-9045-1

    Article  Google Scholar 

  • Andersson L (2001) Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet 2:130–138. doi:10.1038/35052563

    Article  CAS  PubMed  Google Scholar 

  • Andrew RW, Nicolas D, Sean MR, Jérôme SC, Jérôme L, Aurélie L, Arne N, Sébastien R, Julie J, Louis B (2008) The phenomics and expression quantitative trait locus mapping of brain trans-criptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). Genetics 180:147–164. doi:10.1534/genetics.108.089938

    Article  Google Scholar 

  • Aylor DL, Zeng ZB (2008) From classical genetics to quantitative genetics to systems biology: modeling epistasis. PLoS Genet 4(3):e1000029. doi:10.1371/journal.pgen.1000029

    Article  PubMed  Google Scholar 

  • Bao L, Wei L, Peirce JL, Homayouni R, Li HQ, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D, Cui Y (2006) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mamm Genome 17:575–583. doi:10.1007/s00335-005-0172-2

    Article  CAS  PubMed  Google Scholar 

  • Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5, 700 gene expression traits in yeast. PNAS 102(5):1572–1577. doi:10.1073/pnas.0408709102

    Article  CAS  PubMed  Google Scholar 

  • Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296:752–755. doi:10.1126/science.1069516

    Article  CAS  PubMed  Google Scholar 

  • Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169(2):1133–1146. doi:10.1534/genetics.104.035212

    Article  CAS  PubMed  Google Scholar 

  • Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang JT, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke MP, de Haan G (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet 37:225–232. doi:10.1038/ng1497

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Kendziorski C (2007) A statistical framework for expression quantitative trait loci mapping. Genetics 177:761–771. doi:10.1534/genetics.107.071407

    Article  PubMed  Google Scholar 

  • Chen L, Tong TJ, Zhao HY (2008) Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics 24(18):2015–2022. doi:10.1093/bioinformatics/btn373

    Article  CAS  PubMed  Google Scholar 

  • Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, Threadgill DW, Manly KF, Williams RW (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37:233–242. doi:10.1038/ng1518

    Article  CAS  PubMed  Google Scholar 

  • Chesler EJ, Miller DR, Branstetter LR, Galloway LD, Jackson BL, Vivek MP, Voy BH, Culiat CT, Threadgill DW, Williams RW, Churchill GA, Johnson DK, Manly KF (2008) The Collabora-tive Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics. Mamm Genome 19:382–389. doi:10.1007/s00335-008-9135-8

    Article  PubMed  Google Scholar 

  • Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O’Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpää MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FPM, Warden C, Whatley S, Williams RW, Tim Wiltshire T, Yi N, Zhang D, Zhang M, Zou F (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133–1137. doi:10.1038/ng1104-1133

    Article  CAS  PubMed  Google Scholar 

  • Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Heniloff S (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786. doi:10.1111/j.0960-7412.2003.01999.x

    Article  CAS  PubMed  Google Scholar 

  • Daniel MG, Alison HH, Fred AW, David WT, Ivan R (2009a) Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome 20:437–446. doi:10.1007/s00335-009-9199-0

    Article  Google Scholar 

  • Daniel MG, Andrey AS, Tieu-Chong L, Fred AW, Ivan R, Andrew BN (2009b) FastMap: fast eQTL mapping in homozygous populations. Bioinformatics 25(4):482–489. doi:10.1093/bioinformatics/btn648

    Article  Google Scholar 

  • Daniel CC, Lu L, Khyobeni M, Xusheng W, Manjunatha J, John AM, William LT, Klaus D, Perikles S, Robert WW (2010) Detection, validation, and downstream analysis of allelic variation in gene expression. Genetics 184:119–128. doi:10.1534/genetics.109.107474

    Article  Google Scholar 

  • David WT (2006) Meeting report for the 4th annual complex trait consortium meeting: from QTLs to systems genetics. Mamm Genome 17:2–4. doi:10.1007/s00335-005-0153-5

    Article  Google Scholar 

  • de Koning DJ, Haley CS (2005) Genetical genomics in humans and model organisms. Trends Genet 21(7):377–381

    Article  PubMed  Google Scholar 

  • Derome N, Bougas B, Rogers SM, Whiteley AR, Labbe A, Laroche J, Bernatchez L (2008) Pervasive sex-linked effects on transcription regulation as revealed by expression quantitative trait loci mapping in lake whitefish species pairs (Coregonus sp., salmonidae). Genetics 179:1903–1917. doi:10.1534/genetics.107.086306

    Article  CAS  PubMed  Google Scholar 

  • Dinanath S, Alex R, Mark D, Michael W, Veronika N, Ian F, Natalia M (2005) GNARE: automated system for high- throughput genome analysis with Grid computational backend. J Clin Monit Comput 19:361–369. doi:10.1007/s10877-005-3463-y

    Article  Google Scholar 

  • Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3:43–52. doi:10.1038/nrg703

    Article  CAS  PubMed  Google Scholar 

  • Doss S, Schadt EE, Drake TA, Lusis AJ (2005) Cis-acting expres-sion quantitative trait loci in mice. Genome Res 15:681–691. doi:10.1101/gr.3216905

    Article  CAS  PubMed  Google Scholar 

  • Farrall M (2004) Quantitative genetic variation: a post-modern view. Hum Mol Genet 13(1):1R–R7. doi:10.1093/hmg/ddh084

    Article  Google Scholar 

  • Flint J, Valdar W, Shifman S, Mott R (2005) Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev Genet 6:271–285. doi:10.1038/nrg1576

    Article  CAS  PubMed  Google Scholar 

  • Gelfond J, Ibrahim J, Zou F (2007) Proximity model for expression quantitative trait loci (eQTL) detection. Biometrics 63:1108–1116. doi:10.1111/j.1541-0420.2007.00778.x

    CAS  PubMed  Google Scholar 

  • Gilad Y, Rifkin SA, Pritchard JK (2008) Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet 24:408–415. doi:10.1016/j.tig.2008.06.001

    Article  CAS  PubMed  Google Scholar 

  • Gowda M, Venu RC, Roopalakshmi K, Sreerekha MV, Kulkarni RS (2003) Advances in rice breeding, genetics and genomics. Mol Breeding 11:337–352

    Article  CAS  Google Scholar 

  • Hao K, Schadt EE, Storey JD (2008) Calibrating the performance of SNP arrays for whole-genome association studies. PLoS Genet 4(6):e1000109. doi:10.1371/journal.pgen.1000109

    Article  PubMed  Google Scholar 

  • Hill AE, Lander ES, Nadeau JH (2006) Chromosome substitution strains:a new way to study genetically complex traits. Methods Mol Med 128:153–172

    PubMed  Google Scholar 

  • Hitzemann B, Dains K, Kanes S, Hitzemann R (1994) Further studies on the relationship between dopamine cell density and haloperidol-induced catalepsy. J Pharmacol Exp Ther 271:969–976

    CAS  PubMed  Google Scholar 

  • Hu XX, Gao Y, Feng CG QY, Wang XB, Du Z, Wang QS, Li N (2009) Advanced technologies for genomic analysis in farm animals and its application for QTL mapping. Genetica 136:371–386. doi:10.1007/s10709-008-9338-7

    Article  CAS  PubMed  Google Scholar 

  • Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Müller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 37:243–253. doi:10.1038/ng1522

    Article  CAS  PubMed  Google Scholar 

  • Hudgins CC, Steinberg RT, Klinman DM, Reeves MJ, Steinberg AD (1985) Studies of Consomic mice bearing the Y chromosome of the BXSB mouse. J Immunol 134(6):3849–3854

    CAS  PubMed  Google Scholar 

  • Hyonho C, Sündüz K (2009) Expression quantitative trait loci map- ping with multivariate sparse partial least squares regression. Genetics 182:79–90. doi:10.1534/genetics.109.100362

    Article  Google Scholar 

  • Iakoubova OA, Olsson CL, Dains KM, Ross DA, Andalibi A, Lau K, Choi J, Kalcheva I, Cunanan M, Louie J, Nimon V, Machrus M, Bentley LG, Beauheim C, Silvery S, Cavalcoli J, Lusis AJ, West DB (2001) Genome-tagged mice (GTM): two sets of genome-wide congenic strains. Genomics 74:89–104. doi:10.1006/geno.2000.6497

    Article  CAS  PubMed  Google Scholar 

  • Ideker T, Winslow LR, Lauffenburger AD (2006) Bioengineering and systems biology. Ann Biomed Eng 34(2):257–264. doi:10.1007/s10439-005-9047-7

    Article  PubMed  Google Scholar 

  • Jansen RC (2003) Studying complex biological systems using multifactorial perturbation. Nat Rev Genet 4:145–151. doi:10.1038/nrg996

    Article  CAS  PubMed  Google Scholar 

  • Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17(7):388–391. doi:10.1016/S0168-9525(01)02310-1

    Article  CAS  PubMed  Google Scholar 

  • Jia ZY, Xu SZ (2007) Mapping quantitative trait loci for expression abundance. Genetics 176:611–623. doi:10.1534/genetics.106.065599

    Article  CAS  PubMed  Google Scholar 

  • Kendziorski C, Wang P (2006) A review of statistical methods for expression quantitative trait loci mapping. Mamm Genome 17:509–517. doi:10.1007/s00335-005-0189-6

    Article  PubMed  Google Scholar 

  • Kendziorski C, Newton M, Lan H, Gould M (2003) On parametric empirical bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 22:3899–3914. doi:10.1002/sim.1548

    Article  CAS  PubMed  Google Scholar 

  • Kendziorski CM, Chen M, Yuan M, Lan H, Attie AD (2006) Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62:19–27. doi:10.1111/j.1541-0420.2005.00437.x

    Article  CAS  PubMed  Google Scholar 

  • Keurentjes JJB, Fu JY, Terpstra IR, Garcia JM, van den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC (2007) Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. PNAS 104(5):1708–1713. doi:10.1073/pnas.0610429104

    Article  CAS  PubMed  Google Scholar 

  • Khlestkina EK, Salina EA (2006) SNP Markers: methods of analysis, ways of development, and comparison on an example of common wheat. Russ J Genet 42(6):585–594. doi:10.1134/S1022795406060019

    Article  CAS  Google Scholar 

  • Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe’er D, Koller D (2009) Learning a prior on regulatory potential from eQTL data. PLoS Genet 5(1):e1000358. doi:10.1371/journal.pgen.1000358

    Article  PubMed  Google Scholar 

  • Li J, Burmeister M (2005) Genetical genomics: combining genetics with gene expression analysis. Hum Mol Genet 14:R163–R169. doi:10.1093/hmg/ddi267

    Article  CAS  PubMed  Google Scholar 

  • Liu B, de la Fuente A, Hoeschele I (2008) Gene network inference via structural equation modeling in genetical genomics experiments. Genetics 178:1763–1776. doi:10.1534/genetics.107.080069

    Article  PubMed  Google Scholar 

  • Marilyn ALW, Kyunga K, Daniel JK, van Hans L, Richard WM, Doerge RW, Dina ASC (2007) Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in arabidopsis. Genetics 175:1441–1450. doi:10.1534/genetics.106.064972

    Google Scholar 

  • Martin H, Hans PM, Albrecht EM, Matthias F (2008) The Plabsoft database: a comprehensive database management system for integrating phenotypic and genomic data in academic and commercial plant breeding programs. Euphytica 161:173–179. doi:10.1007/s10681-007-9478-3

    Article  Google Scholar 

  • Matias K, Christopher JB, Alexander AM, Zhao-Bang Z, Ronald RS (2005) Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid. Genetics 169:2295–2303. doi:10.1534/genetics.104.039198

    Article  Google Scholar 

  • Meng H, Vera I, Che N, Wang X, Wang SS, Ingram-Drake L, Schadt EE, Drake TA, Lusis AJ (2007) Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. PNAS 104(11):4530–4535. doi:10.1073/pnas.0607620104

    Article  CAS  PubMed  Google Scholar 

  • Monks SA, Leonardson A, Zhu H, Cundiff P, Pietrusiak P, Edwards S, Phillips JW, Sachs A, Schadt EE (2004) Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 75:1094–1105. doi:10.1086/426461

    Article  CAS  PubMed  Google Scholar 

  • Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430:743–747. doi:10.1038/nature02797

    Article  CAS  PubMed  Google Scholar 

  • Nadeau JH, Singer JB, Matin A, Lander ES (2000) Analysing complex genetic traits with chromosome substitution strains. Nat Genet 24(3):221–225. doi:10.1038/73427

    Article  CAS  PubMed  Google Scholar 

  • Nan B, Ina H (2005) Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 170:533–542. doi:10.1534/genetics.105.041103

    Article  Google Scholar 

  • Newton M, Kendziorski C, Richmond C, Blattner F, Tsui K (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol 8:37–52. doi:10.1089/106652701300099074

    Article  CAS  PubMed  Google Scholar 

  • Noble D (2002) Modeling the heart—from genes to cells to the whole organ. Science 295:1678–1682. doi:10.1126/science.1069881

    Article  CAS  PubMed  Google Scholar 

  • Paigen K, Eppig JT (2000) A mouse phenome project. Mamm Genome 11(9):715–717. doi:10.1007/s003350010152

    Article  CAS  PubMed  Google Scholar 

  • Paul S (2008) Statistical power of expression quantitative trait loci for mapping of complex trait loci in natural populations. Genetics 178:2201–2216. doi:10.1534/genetics.107.076687

    Article  Google Scholar 

  • Peters LL, Robledo RF, Bult CJ, Churchill GA, Paigen BJ, Svenson KL (2007) The mouse as a model for human biology: a resource guide for complex trait analysis. Nat Rev Genet 8:58–59. doi:10.1038/nrg2025

    Article  CAS  PubMed  Google Scholar 

  • Phillip M, Jeff J, Chunlei W, David LD, John RW, Serge B, Joseph ST, Kazuhiro S, Akira K, Joseph B, Tim W, Andrew IS (2007) Genomewide association analysis in diverse inbred mice: power and population structure. Genetics 176:675–683. doi:10.1534/genetics.106.066241

    Article  Google Scholar 

  • Potokina EK, Druka A, Luo Z, Waugh R, Kearsey MJ (2009) The transcriptome analysis of barley (Hordeum vulgare L.) using the Affymetrix Barley1 GeneChip. Russ J Genet 45(11):1317–1328. doi:10.1134/S1022795409110064

    Article  CAS  Google Scholar 

  • Prem N (2010) Quantitative genetics: past and present. Mol Breeding 26(2):135–146. doi:10.1007/s11032-010-9406-4

    Article  Google Scholar 

  • Rhonda DC, Sonia L, Dan N, Stephen HH (2006) Genetic regulation of gene expression during shoot development in arabidopsis. Genetics 172:1155–1164. doi:10.1534/genetics.105.042275

    Google Scholar 

  • Rockman MV, Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7:862–872. doi:10.1038/nrg1964

    Article  CAS  PubMed  Google Scholar 

  • Rudi B (2007) From mouse genetics to systems biology. Mamm Genome 18:383–388. doi:10.1007/s00335-007-9044-2

    Article  Google Scholar 

  • Sasaki T, Antonio B (2005) Where does the accurate rice genome sequence lead us? Plant Mol Biol 59:27–32. doi:10.1007/s11103-005-1224-4

    Article  CAS  PubMed  Google Scholar 

  • Satoshi Y, Kuniko W, Tomoko N, Yoshimi T, Takashi K, Toshikazu U (2005) Expression quantitative trait loci analysis of 13 genes in the rat prostate. Genetics 171:1231–1238. doi:10.1534/genetics.104.038174

    Article  Google Scholar 

  • Schadt EE, Lum PY (2006) Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. reverse engineering gene networks to identify key drivers of complex disease phenotypes. J Lipid Res 47:2601–2613. doi:10.1194/jlr.R600026-JLR200

    Article  CAS  PubMed  Google Scholar 

  • Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422:297–302. doi:10.1038/nature01434

    Article  CAS  PubMed  Google Scholar 

  • Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6(5):1020–1032. doi:10.1371/journal.pbio.0060107

    Article  CAS  Google Scholar 

  • Schadt EE, Zhang B, Zhu J (2009) Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments. Genetica 136:259–269. doi:10.1007/s10709-009-9359-x

    Article  CAS  PubMed  Google Scholar 

  • Shi C, Uzarowska A, Ouzunova M, Landbeck M, Wenzel G, Lübberstedt T (2007) Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci)analysis in a Flint X Flint maize recombinant inbred line population. BMC Genomics 8:22. doi:10.1186/1471-2164-8-22

    Article  PubMed  Google Scholar 

  • Sieberts SK, Schadt EE (2007) Moving toward a system genetics view of disease. Mamm Genome 18:389–401. doi:10.1007/s00335-007-9040-6

    Article  PubMed  Google Scholar 

  • Silpa S, Andreas B, Richard MK, Yonina E, Trey I (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Sys Biol 4:162. doi:10.1038/msb.2008.4

    Google Scholar 

  • Storey JD, Akey JM, Kruglyak L (2005) Multiple locus linkage analysis of genome-wide expression in yeast. PLoS Biol 3(8):1380–1390. doi:10.1371/journal.pbio.0030267

    Article  CAS  Google Scholar 

  • Su WL, Sieberts SK, Kleinhanz RR, Lux K, Millstein J, Molony C, Schadt EE (2010) Assessing the prospects of genome-wide association studies performed in inbred mice. Mamm Genome 21:143–152. doi:10.1007/s00335-010-9249-7

    Article  PubMed  Google Scholar 

  • Sun W, Yu TW, Li KC (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23(17):2290–2297. doi:10.1093/bioinformatics/btm327

    Article  CAS  PubMed  Google Scholar 

  • Sun W, Yuan SS, Li KC (2008) Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC Genomics 9:242. doi:10.1186/1471-2164-9-242

    Article  PubMed  Google Scholar 

  • Todd ES, Kwang-Youn AK, Ruth ES, Alisdair RP, Terry AB, Kevin LK, Anne MD, Gerald FD, Jian H, Thomas LC, Val CS, Edwin MS (2006) Regulation of gene expression in the mammalian eye and its relevance to eye disease. PNAS 103(39):14429–14434. doi:10.1073/pnas.0602562103

    Article  Google Scholar 

  • Tusher V, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98:5116–5121. doi:10.1073/pnas.091062498

    Article  CAS  PubMed  Google Scholar 

  • Valdar W, Solberg LC, Gauguier D, Burnett S, Klenerman P, Cookson WO, Taylor MS, Rawlins JNP, Mott R, Flint J (2006) Genome-wide genetic association of complex traits in hetero- geneous stock mice. Nat Genet 38(8):879–887. doi:10.1038/ng1840

    Article  CAS  PubMed  Google Scholar 

  • Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270. doi:10.1007/s00122-006-0227-0

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Yehya N, Schadt EE, Wang H, Drake TA, Lusis AJ (2006) Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet 2(2):0148–0159. doi:10.1371/journal.pgen.0020015

    Article  CAS  Google Scholar 

  • Wittkopp PJ (2005) Genomic sources of regulatory variation in cis and in trans. Cell Mol Life Sci 62:1779–1783. doi:10.1007/s00018-005-5064-9

    Article  CAS  PubMed  Google Scholar 

  • Wu CL, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, Walker JR, Glynne RJ, Cooke MP, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Saez E, Wiltshire T, Su AI (2008) Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet 4(5):e1000070. doi:10.1371/journal.pgen.1000070

    Article  PubMed  Google Scholar 

  • Xu YB, McCouch SR, Zhang QF (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26. doi:10.1007/s11103-004-4681-2

    Article  CAS  PubMed  Google Scholar 

  • Yan F, Tsui-Jung W, Yefim IR, Hsin DC, Ling G, David IM, Hsin DC, Ling G, David IM, Yongjie Y, Michael L, Abraham BK, Daniel AA, Patrick SS (2006) Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174:1671–1683. doi:10.1534/genetics.106.060376

    Article  Google Scholar 

  • Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35(1):57–64. doi:10.1038/ng1222

    Article  CAS  PubMed  Google Scholar 

  • Zou W, Zeng ZB (2009) Multiple interval mapping for gene expression QTL analysis. Genetica 137:125–134. doi:10.1007/s10709-009-9365-z

    Article  CAS  PubMed  Google Scholar 

  • Zou F, Gelfond JA, Airey DC, Lu L, Manly KF, Robert W, Williams RW, Threadgill DW (2005) Quantitative trait locus analysis using recombinant inbred intercrosses: theoretical and empirical considerations. Genetics 170:1299–1311. doi:10.1534/genetics.104.035709

    Article  CAS  PubMed  Google Scholar 

  • Zou W, Aylor DL, Zeng ZB (2007) eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics 8:7. doi:10.1186/1471-2105-8-7

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Environmental and Biological Engineering, Chongqing Technology and Business University, 400067, Chongqing, China

    Hong Li

  2. Osteoporsis Research Center and Department of Biomedical Science, Creighton University, Omaha, NE, 68313, USA

    Hongwen Deng

Authors
  1. Hong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hongwen Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hong Li.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, H., Deng, H. Systems genetics, bioinformatics and eQTL mapping. Genetica 138, 915–924 (2010). https://doi.org/10.1007/s10709-010-9480-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10709-010-9480-x

Keywords

Search

Navigation