Systems genetics, bioinformatics and eQTL mapping.
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.
Li
Hong
H
College of Environmental and Biological Engineering, Chongqing Technology and Business University, 400067 Chongqing, China. cqgsdxlh@163.com
Deng
Hongwen
H
D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D040641:Quantitative Trait Loci
Bioinformatics. 2008 Sep 15;24(18):2015-22
18635565
PLoS Biol. 2005 Aug;3(8):e267
16035920
PLoS Genet. 2008 Jun 27;4(6):e1000109
18584036
J Immunol. 1985 Jun;134(6):3849-54
3989299
PLoS Genet. 2008 Mar 14;4(3):e1000029
18369448
Genetics. 2007 May;176(1):675-83
17409088
Mamm Genome. 2005 May;16(5):291-305
16104378
PLoS Biol. 2008 May 6;6(5):e107
18462017
Cell Mol Life Sci. 2005 Aug;62(16):1779-83
15968467
J Pharmacol Exp Ther. 1994 Nov;271(2):969-76
7965819
Genetica. 2009 Nov;137(2):125-34
19430916
Methods Mol Med. 2006;128:153-72
17071995
Mamm Genome. 2009 Jul;20(7):437-46
19609828
Mamm Genome. 2008 Jun;19(6):382-9
18716833
Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1572-7
15659551
Nat Genet. 2000 Mar;24(3):221-5
10700173
Nat Genet. 2003 Sep;35(1):57-64
12897782
Plant Mol Biol. 2005 Sep;59(1):27-32
16217599
Science. 2002 Apr 26;296(5568):752-5
11923494
BMC Genomics. 2007 Jan 18;8:22
17233901
Mamm Genome. 2006 Jan;17(1):2-4
16416085
Mamm Genome. 2006 Jun;17(6):509-17
16783633
Nat Genet. 2004 Nov;36(11):1133-7
15514660
Nat Genet. 2005 Mar;37(3):225-32
15711547
Genetics. 2007 Mar;175(3):1441-50
17179097
Genetics. 2007 May;176(1):611-23
17339210
Genetika. 2006 Jun;42(6):725-36
16871776
Nature. 2004 Aug 12;430(7001):743-7
15269782
Nat Genet. 2006 Aug;38(8):879-87
16832355
Nat Rev Genet. 2005 Apr;6(4):271-86
15803197
Nat Genet. 2005 Mar;37(3):243-53
15711544
Biometrics. 2007 Dec;63(4):1108-16
17425636
Genetics. 2008 Apr;178(4):2201-16
18245851
Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1708-13
17237218
Theor Appl Genet. 2006 May;112(7):1258-70
16477428
Genetics. 2007 Oct;177(2):761-71
17660576
BMC Genomics. 2008 May 23;9:242
18498664
Mamm Genome. 2007 Jul;18(6-7):473-81
17674098
Genome Res. 2005 May;15(5):681-91
15837804
Biometrics. 2006 Mar;62(1):19-27
16542225
BMC Bioinformatics. 2007 Jan 09;8:7
17212828
Nat Rev Genet. 2003 Feb;4(2):145-51
12560811
Genetika. 2009 Nov;45(11):1493-505
20058796
Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14429-34
16983098
Nat Rev Genet. 2007 Jan;8(1):58-69
17173058
Genomics. 2001 May 15;74(1):89-104
11374905
Plant Mol Biol. 2005 Sep;59(1):7-26
16217598
Bioinformatics. 2007 Sep 1;23(17):2290-7
17599927
Science. 2002 Mar 1;295(5560):1678-82
11872832
Genetics. 2005 Jul;170(3):1299-311
15879512
Genetics. 2005 Nov;171(3):1231-8
16079240
Genetics. 2006 Feb;172(2):1155-64
15956669
Nat Rev Genet. 2001 Feb;2(2):130-8
11253052
Genetics. 2006 Nov;174(3):1671-83
16951074
J Clin Monit Comput. 2005 Oct;19(4-5):361-9
16328950
Genetica. 2009 Jun;136(2):371-86
19093212
Genetics. 2010 Jan;184(1):119-28
19884314
Mol Syst Biol. 2008;4:162
18319721
Genetics. 2005 Jun;170(2):533-42
15781693
Genetics. 2008 Mar;178(3):1763-76
18245846
Genetica. 2009 Jun;136(2):259-69
19363597
Genetics. 2008 Aug;179(4):1903-17
18660540
Nat Rev Genet. 2002 Jan;3(1):43-52
11823790
Genetics. 2005 Apr;169(4):2295-303
15687266
Stat Med. 2003 Dec 30;22(24):3899-914
14673946
Trends Genet. 2008 Aug;24(8):408-15
18597885
Mamm Genome. 2000 Sep;11(9):715-7
10967127
Bioinformatics. 2009 Feb 15;25(4):482-9
19091771
Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4530-5
17360558
Nat Genet. 2005 Mar;37(3):233-42
15711545
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
11309499
Mamm Genome. 2006 Jun;17(6):575-83
16783639
PLoS Genet. 2008 May 09;4(5):e1000070
18464898
Ann Biomed Eng. 2006 Feb;34(2):257-64
16474915
Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R163-9
16244315
J Lipid Res. 2006 Dec;47(12):2601-13
17012750
Plant J. 2004 Mar;37(5):778-86
14871304
Genetics. 2008 Sep;180(1):147-64
18757926
Trends Genet. 2001 Jul;17(7):388-91
11418218
Mamm Genome. 2010 Apr;21(3-4):143-52
20135320
Genetics. 2009 May;182(1):79-90
19270271
Genetics. 2005 Feb;169(2):1133-46
15545647
J Comput Biol. 2001;8(1):37-52
11339905
Nat Rev Genet. 2006 Nov;7(11):862-72
17047685
Nature. 2003 Mar 20;422(6929):297-302
12646919
PLoS Genet. 2006 Feb;2(2):e15
16462940
Mamm Genome. 2007 Jul;18(6-7):389-401
17653589
PLoS Genet. 2009 Jan;5(1):e1000358
19180192
Hum Mol Genet. 2004 Apr 1;13 Spec No 1:R1-7
14962979
Mamm Genome. 2007 Jul;18(6-7):383-8
17668264
Am J Hum Genet. 2004 Dec;75(6):1094-105
15514893
Trends Genet. 2005 Jul;21(7):377-81
15908034