title: Chapter 15: disease gene prioritization.
abstract: Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases.
authors: Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA. YanaB@rci.rutgers.edu
authors: Yana
authors: Y
authors: Bromberg
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005091:Exons; D020022:Genetic Predisposition to Disease; D005823:Genetics; D006801:Humans; D008962:Models, Theoretical; D009154:Mutation; D010641:Phenotype; D025941:Protein Interaction Mapping; D012984:Software
references: Bioinformatics. 2008 Oct 15;24(20):2397-8
references: 18757876
references: Bioinformatics. 2010 Oct 1;26(19):2458-9
references: 20685956
references: Bioinformatics. 2012 Feb 15;28(4):601-2
references: 22210871
references: J Mol Biol. 1995 Apr 7;247(4):536-40
references: 7723011
references: Vet Pathol. 2010 Nov;47(6):1016-20
references: 20587689
references: Trends Genet. 2003 May;19(5):238-42
references: 12711213
references: BMC Bioinformatics. 2008 Dec 08;9:528
references: 19063745
references: Methods Mol Biol. 2007;408:153-69
references: 18314582
references: Am J Hum Genet. 2008 Nov;83(5):610-5
references: 18950739
references: Nature. 1983 Nov 17-23;306(5940):234-8
references: 6316146
references: Nature. 2003 Jan 2;421(6918):63-6
references: 12511954
references: Yale J Biol Med. 2001 May-Jun;74(3):179-84
references: 11501714
references: Genet Epidemiol. 2008 Dec;32(8):779-90
references: 18613097
references: Proc Int Conf Intell Syst Mol Biol. 1999;:60-7
references: 10786287
references: Proc Biol Sci. 2004 Jan 7;271(1534):89-96
references: 15002776
references: Hum Genomics. 2009 Oct;4(1):21-42
references: 21072972
references: Nucleic Acids Res. 2003 Jul 1;31(13):3812-4
references: 12824425
references: Bioinformatics. 2008 Apr 1;24(7):1011-3
references: 18204061
references: Bioinformatics. 2010 May 15;26(10):1291-8
references: 20378554
references: Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
references: 10982861
references: PLoS Biol. 2009 Nov;7(11):e1000247
references: 19956802
references: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references: 11752295
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
references: 18158299
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D700-6
references: 17142238
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references: 19920124
references: Am J Hum Genet. 2006 Jun;78(6):1011-25
references: 16685651
references: Hum Genet. 2007 May;121(3-4):501-9
references: 17211639
references: Nat Genet. 2002 Jul;31(3):316-9
references: 12006977
references: Curr Genomics. 2009 Mar;10(1):64-75
references: 19721813
references: Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4695-700
references: 15070780
references: Br Med J (Clin Res Ed). 1984 Feb 11;288(6415):429-30
references: 6229316
references: J Natl Cancer Inst. 1999 Jun 2;91(11):916-32
references: 10359544
references: Nature. 1983 Nov 10-16;306(5939):151-5
references: 6316140
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5
references: 18940856
references: Trends Biotechnol. 2009 Apr;27(4):210-9
references: 19251332
references: Nat Biotechnol. 2006 May;24(5):537-44
references: 16680138
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W212-6
references: 17478516
references: Nat Rev Genet. 2012 Jul 03;13(8):523-36
references: 22751426
references: Nucleic Acids Res. 1999 Jan 1;27(1):355-7
references: 9847227
references: Nucleic Acids Res. 2004 Jun 04;32(10):3108-14
references: 15181176
references: N Engl J Med. 2003 Mar 20;348(12):1085-95
references: 12646665
references: Trends Genet. 1997 Apr;13(4):163
references: 9097728
references: Am J Obstet Gynecol. 2007 Apr;196(4):386.e1-9; discussion 386.e9-11
references: 17403429
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7
references: 21115458
references: Am J Obstet Gynecol. 2010 Sep;203(3):242.e1-5
references: 20605134
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):605-10
references: 12529507
references: BMC Genomics. 2010 Dec 02;11 Suppl 4:S24
references: 21143808
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6
references: 18842627
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references: 19880382
references: J Clin Endocrinol Metab. 2003 Sep;88(9):4258-67
references: 12970296
references: Nat Genet. 2006 Mar;38(3):285-93
references: 16501559
references: Hum Mutat. 2004 Jun;23(6):534-9
references: 15146456
references: Oncogene. 2008 Dec;27 Suppl 2:S9-18
references: 19956182
references: Bioessays. 2007 Jun;29(6):515-9
references: 17508390
references: Nucleic Acids Res. 2006;34(19):e130
references: 17020920
references: Cell. 1997 Jan 10;88(1):131-41
references: 9019399
references: Trends Genet. 2002 Dec;18(12):604-6
references: 12446137
references: Bioinformatics. 2007 May 1;23(9):1132-40
references: 17237041
references: PLoS Comput Biol. 2008 Jan;4(1):e5
references: 18208319
references: J Biol Chem. 2006 Feb 17;281(7):4242-53
references: 16293621
references: Bioinformatics. 2012 Sep 15;28(18):i569-i574
references: 22962483
references: Bioinformatics. 2010 Sep 1;26(17):2208-9
references: 20605930
references: Nucleic Acids Res. 2002 Sep 1;30(17):3894-900
references: 12202775
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D527-32
references: 15608254
references: Eur J Hum Genet. 2008 May;16(5):581-6
references: 18231126
references: Nat Genet. 2004 May;36(5):431-2
references: 15118671
references: Curr Top Behav Neurosci. 2011;6:157-75
references: 21243475
references: J Mol Biol. 2002 Oct 25;323(3):573-84
references: 12381310
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50
references: 20952405
references: Nucleic Acids Res. 2010 Oct;38(18):6102-11
references: 20488869
references: Twin Res Hum Genet. 2007 Dec;10(6):861-70
references: 18179399
references: Nucleic Acids Res. 2007;35(11):3823-35
references: 17526529
references: PLoS Genet. 2008 Mar 14;4(3):e1000014
references: 18369440
references: J Clin Endocrinol Metab. 2004 May;89(5):2028-32
references: 15126516
references: Nature. 2001 Feb 15;409(6822):822-3
references: 11236997
references: J Biol. 2002;1(1):5
references: 12144710
references: Nat Genet. 2007 Oct;39(10):1217-24
references: 17873874
references: Nucleic Acids Res. 2002 Jan 1;30(1):303-5
references: 11752321
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
references: 21097893
references: PLoS Comput Biol. 2010 Jan 15;6(1):e1000641
references: 20090828
references: Bioinformatics. 2004 Oct 12;20(15):2479-81
references: 15073010
references: Bioinformatics. 2005 Nov 15;21(22):4181-6
references: 16179360
references: Science. 1992 Aug 7;257(5071):797-800
references: 1379744
references: J Inherit Metab Dis. 1994;17(1):145-8
references: 8051927
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8
references: 19843607
references: Mol Cell Proteomics. 2010 Apr;9(4):648-55
references: 19959820
references: Genome Res. 2003 Sep;13(9):2178-89
references: 12952885
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W634-7
references: 15215466
references: Nucleic Acids Res. 2000 Jan 1;28(1):45-8
references: 10592178
references: Nat Genet. 2003 Mar;33 Suppl:228-37
references: 12610532
references: Genome Res. 2003 Jun;13(6A):1222-30
references: 12799354
references: Endocrinology. 2007 Oct;148(10):4642-8
references: 17628007
references: BMC Med Genomics. 2010 Oct 13;3:45
references: 20942928
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6
references: 21045057
references: Biochemistry. 2006 Jun 13;45(23):7277-88
references: 16752916
references: Bioinformatics. 2003 Jul 1;19(10):1275-83
references: 12835272
references: Nat Genet. 2004 Jul;36(7):664
references: 15226743
references: Annu Rev Genomics Hum Genet. 2006;7:61-80
references: 16824020
references: Nat Med. 1999 Sep;5(9):1066-70
references: 10470087
references: PLoS Comput Biol. 2008 Oct;4(10):e1000160
references: 18974821
references: Bioinformatics. 2006 Nov 15;22(22):2729-34
references: 16895930
references: Nucleic Acids Res. 2000 Jan 1;28(1):263-6
references: 10592242
references: Science. 1949 Apr 29;109(2835):443
references: 18213804
references: PLoS One. 2008;3(12):e3874
references: 19057649
references: BMC Bioinformatics. 2006 Mar 22;7:166
references: 16551372
references: Mol Biol Evol. 2005 Mar;22(3):767-75
references: 15574806
references: Nature. 1956 Oct 13;178(4537):792-4
references: 13369537
references: Hum Mutat. 2008 Mar;29(3):361-6
references: 18175334
references: BMC Bioinformatics. 2005 Mar 14;6:55
references: 15766383
references: Bioinformatics. 2010 Sep 15;26(18):i561-7
references: 20823322
references: Bioinformatics. 2010 Aug 15;26(16):2069-70
references: 20562413
references: BMC Bioinformatics. 2005;6 Suppl 1:S1
references: 15960821
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D230-4
references: 21071420
references: Am J Hum Genet. 1998 Jul;63(1):52-4
references: 9634529
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W635-41
references: 16845089
references: Methods Mol Biol. 2011;694:49-61
references: 21082427
references: Bioinformatics. 2007 Mar 1;23(5):651-3
references: 17237069
references: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W377-84
references: 18508807
references: Nat Methods. 2010 Apr;7(4):248-9
references: 20354512
references: PLoS Comput Biol. 2008 Mar 28;4(3):e1000043
references: 18369433
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W242-8
references: 15215388
references: BMC Bioinformatics. 2008 Jan 25;9:50
references: 18221506
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D244-8
references: 19923227
references: Nat Genet. 2004 Sep;36(9):949-51
references: 15286789
references: Genome Biol. 2008;9 Suppl 2:S7
references: 18834498
references: Cell. 1993 Mar 26;72(6):971-83
references: 8458085
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704
references: 21071413
references: Nat Genet. 1995 May;10(1):111-3
references: 7647779
references: Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):390-399
references: 20052305
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D161-6
references: 19858104
references: Bioinformatics. 2006 Mar 15;22(6):773-4
references: 16423925
references: Bioinformatics. 2010 Apr 15;26(8):1057-63
references: 20185403
references: Am J Hum Genet. 2008 Apr;82(4):949-58
references: 18371930
references: Hum Mutat. 2003 Jun;21(6):577-81
references: 12754702
references: Genome Res. 1999 Aug;9(8):677-9
references: 10447503
references: BMC Bioinformatics. 2007 Oct 16;8:392
references: 17939863
references: PLoS One. 2010 Oct 22;5(10):e13574
references: 21042586
references: Am J Hum Genet. 2008 Jan;82(1):150-9
references: 18179893
references: Bioinformatics. 2007 May 15;23(10):1274-81
references: 17344234
references: Mutat Res. 2003 Nov;544(2-3):99-106
references: 14644312
references: J Bacteriol. 2009 Jul;191(14):4624-32
references: 19447909
references: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references: 10592173
references: PLoS Genet. 2010 May 20;6(5):e1000962
references: 20502679
references: Eur J Hum Genet. 2006 May;14(5):535-42
references: 16493445
references: Bioinformatics. 2007 Jul 15;23(14):1862-5
references: 17495998
references: Bioinformatics. 2009 Mar 1;25(5):655-61
references: 19098027
references: Proteins. 2008 Aug 15;72(3):1030-7
references: 18300252
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22
references: 18981052
references: BMC Genomics. 2004 Jan 13;5(1):4
references: 14718066
references: Brief Bioinform. 2011 Jan;12(1):22-32
references: 21278374
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W321-6
references: 15215403
references: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405
references: 18487273
references: Adv Genet. 2010;70:201-43
references: 20920750
references: AMIA Annu Symp Proc. 2003;:460-4
references: 14728215
references: Bioinformatics. 2009 Jun 15;25(12):i222-30
references: 19477992
references: DNA Res. 2010 Jun;17(3):197-208
references: 20360267
references: Genome Biol. 2005;6(1):R7
references: 15642099
references: Bioinformatics. 2002 Dec;18(12):1681-5
references: 12490454
references: J Biol Chem. 1989 Dec 15;264(35):21376-80
references: 2531748
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11
references: 19465376
references: BMC Genomics. 2010 Dec 01;11 Suppl 3:S5
references: 21143787
references: Nat Protoc. 2009;4(7):1073-81
references: 19561590
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4
references: 21071405
references: Hum Mutat. 2004 Aug;24(2):112-9
references: 15241792
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
references: 18940858
references: Genomics. 2008 Mar;91(3):243-8
references: 18082363