Integrating physical and genetic maps: from genomes to interaction networks.
Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual interaction measurements into contiguous pathway models; and annotating these pathways with detailed functional information. A particular challenge involves reconciling the wide variety of interaction types that are currently available. For this purpose, recent studies have sought to classify genetic and physical interactions along several complementary dimensions, such as ordered versus unordered, alleviating versus aggravating, and first versus second degree.
Beyer
Andreas
A
Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
Bandyopadhyay
Sourav
S
Ideker
Trey
T
D053263:Gene Regulatory Networks; D005821:Genetic Techniques; D015894:Genome, Human; D006801:Humans; D008954:Models, Biological; D020161:Physical Chromosome Mapping; D015398:Signal Transduction / Q000235:genetics
Nat Genet. 2007 Feb;39(2):199-206
17206143
BMC Bioinformatics. 2006;7:360
16872496
Nat Genet. 2005 Jul;37(7):710-7
15965475
Science. 2000 Dec 22;290(5500):2306-9
11125145
Nature. 2002 Jan 10;415(6868):141-7
11805826
Trends Genet. 1992 Sep;8(9):312-6
1365397
Genome Res. 2006 Oct;16(10):1299-309
16954542
Nat Biotechnol. 2006 Nov;24(11):1429-35
16998473
Nat Genet. 2005 Jan;37(1):77-83
15592468
Biochem Soc Trans. 2003 Dec;31(Pt 6):1513-5
14641101
Cell. 2006 Jun 16;125(6):1193-205
16777607
Pharmacogenomics. 2003 Jan;4(1):67-79
12517287
Nat Protoc. 2006;1(3):1617-20
17406454
J Biol. 2005;4(2):6
15982408
Annu Rev Biochem. 1987;56:89-124
2441660
BMC Neurosci. 2006;7 Suppl 1:S10
17118154
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
9843981
Bioinformatics. 2006 Jul 15;22(14):e489-96
16873511
Science. 2004 Jan 23;303(5657):540-3
14704431
Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74
11283351
BMC Genomics. 2006;7:187
16869964
Cell. 2005 Aug 26;122(4):517-27
16122420
Science. 2004 Nov 26;306(5701):1555-8
15567862
Science. 2001 Dec 14;294(5550):2364-8
11743205
Cell. 2000 Jul 7;102(1):109-26
10929718
Nature. 2006 Mar 30;440(7084):637-43
16554755
Trends Genet. 2001 Jun;17(6):346-52
11377797
Nat Rev Genet. 2007 Jun;8(6):437-49
17510664
Theor Appl Genet. 1972 Jan;42(3):119-24
24430832
Nature. 1975 Jun 26;255(5511):680-4
1169690
Mol Cell Biol. 1995 Oct;15(10):5820-9
7565735
Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285-8
10200254
Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):793-8
14718668
Nature. 2005 Oct 20;437(7062):1173-8
16189514
J Bacteriol. 1993 Oct;175(20):6377-81
8407814
Nature. 2003 Mar 20;422(6929):297-302
12646919
Mamm Genome. 2006 Jun;17(6):575-83
16783639
Nature. 2005 Aug 11;436(7052):861-5
16094371
Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14718-23
17003128
Proteomics. 2005 May;5(8):2082-9
15832363
Cell. 2006 Jan 13;124(1):207-19
16413492
Genetics. 1998 Jul;149(3):1167-71
9649511
Nat Biotechnol. 2005 Aug;23(8):975-82
16025103
Science. 2005 Mar 11;307(5715):1621-5
15761153
Genome Res. 2006 Dec;16(12):1445-54
17053092
Nat Neurosci. 2004 May;7(5):485-6
15114364
Cell. 2006 Mar 10;124(5):1069-81
16487579
Nat Genet. 2007 May;39(5):683-7
17417638
Eur J Hum Genet. 2007 Mar;15(3):260-3
17164797
Nature. 2001 Feb 15;409(6822):951-3
11237020
Genome Biol. 2006;7(7):R63
16859555
Mol Syst Biol. 2006;2:2006.0012
16738557
Genome Res. 2007 Jul;17(7):1061-71
17513831
Nat Biotechnol. 2007 Mar;25(3):309-16
17344885
Science. 2004 Feb 6;303(5659):808-13
14764870
Nat Genet. 2006 Apr;38(4):431-40
16518401
Genome Res. 2001 Oct;11(10):1758-65
11591653
Science. 2003 Dec 5;302(5651):1727-36
14605208
Nature. 2004 Sep 2;431(7004):99-104
15343339
FEBS J. 2005 Nov;272(21):5391-9
16262681
Cell. 2005 Mar 11;120(5):715-27
15766533
Nature. 2005 Dec 1;438(7068):679-84
16319894
BMC Bioinformatics. 2003 Jan 13;4:2
12525261
Mol Syst Biol. 2005;1:2005.0026
16729061
Genome Res. 2006 Apr;16(4):520-6
16533914
Genome Biol. 2005;6(4):R38
15833125
Nat Genet. 2003 Nov;35(3):277-86
14566339
Nature. 2007 Apr 12;446(7137):806-10
17314980
Genome Biol. 2005;6(7):R62
15998451
Nature. 2006 Mar 30;440(7084):631-6
16429126
Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6579-84
17420474
PLoS Comput Biol. 2006 Jun 16;2(6):e70
16789814
Science. 1997 Oct 24;278(5338):605-7
9381170
Science. 1990 Oct 12;250(4978):245-50
2218528
Nat Biotechnol. 2006 Apr;24(4):427-33
16601728
Nat Methods. 2006 Nov;3(11):881-6
17060911
Nature. 2005 Aug 4;436(7051):701-3
16079846
Cell. 1988 Aug 12;54(4):541-52
3135940
Science. 2007 Jun 29;316(5833):1840-2
17605173
Nature. 2000 Feb 10;403(6770):623-7
10688190
Mol Syst Biol. 2007;3:104
17437029
Science. 2001 Feb 16;291(5507):1195
11233436
Science. 2001 May 4;292(5518):929-34
11340206
Nat Genet. 2006 Aug;38(8):896-903
16845399
Science. 2002 Feb 15;295(5558):1306-11
11847345
Mol Syst Biol. 2007;3:96
17389876
Nature. 2002 May 23;417(6887):399-403
12000970
Cytogenet Cell Genet. 2001;93(1-2):1-10
11474168
Nat Rev Genet. 2003 Feb;4(2):145-51
12560811
Nat Biotechnol. 2000 Apr;18(4):424-8
10748524
Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1283-8
17227853
Nucleic Acids Res. 2007 Jan;35(Database issue):D198-201
17145705
Cell. 2005 Sep 23;122(6):957-68
16169070
Science. 2003 Oct 10;302(5643):249-55
12934013
Genome Res. 2004 Oct;14(10B):2093-101
15489331
Mol Cell Proteomics. 2007 Mar;6(3):439-50
17200106
Mol Cell. 2004 Feb 27;13(4):469-82
14992718
Cell. 2005 Nov 4;123(3):507-19
16269340
PLoS Genet. 2006 Oct 20;2(10):e172
17054398
Nat Biotechnol. 2005 Aug;23(8):951-9
16082366
Nature. 2001 Jan 25;409(6819):533-8
11206552
Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4143-4
11904394
Curr Opin Struct Biol. 2004 Jun;14(3):292-9
15193308
Nat Rev Genet. 2001 Jul;2(7):493-503
11433356
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4372-6
12676999
Bioinformatics. 2006 Apr 1;22(7):823-9
16455753
Genome Res. 1998 Mar;8(3):175-85
9521921
Proteomics. 2006 Oct;6(20):5374-84
16991196
Nat Protoc. 2006;1(1):302-7
17406249
J Lipid Res. 2006 Dec;47(12):2601-13
17012750
Nat Biotechnol. 2005 May;23(5):561-6
15877074
J Comput Biol. 2004;11(2-3):243-62
15285891
Science. 2006 May 19;312(5776):1054-9
16709784