Integrating multiple microarray data for cancer pathway analysis using bootstrapping K-S test.
Previous applications of microarray technology for cancer research have mostly focused on identifying genes that are differentially expressed between a particular cancer and normal cells. In a biological system, genes perform different molecular functions and regulate various biological processes via interactions with other genes thus forming a variety of complex networks. Therefore, it is critical to understand the relationship (e.g., interactions) between genes across different types of cancer in order to gain insights into the molecular mechanisms of cancer. Here we propose an integrative method based on the bootstrapping Kolmogorov-Smirnov test and a large set of microarray data produced with various types of cancer to discover common molecular changes in cells from normal state to cancerous state. We evaluate our method using three key pathways related to cancer and demonstrate that it is capable of finding meaningful alterations in gene relations.
Han
Bing
B
Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA.
Chen
Xue-Wen
XW
Wang
Xinkun
X
Michaelis
Elias K
EK
D048708:Cell Growth Processes / Q000502:physiology; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction; D051785:Smad Proteins / Q000235:genetics / Q000378:metabolism; D018709:Statistics, Nonparametric
D051785:Smad Proteins
J Biol Chem. 2000 Feb 25;275(8):5485-92
10681527
Bioinformatics. 2006 Jun 1;22(11):1367-74
16543279
Bioinformatics. 2003 Jun 12;19(9):1046-54
12801864
Nature. 2005 Oct 20;437(7062):1173-8
16189514
J Biol Chem. 2001 Oct 26;276(43):39608-17
11546783
Science. 1997 Oct 24;278(5338):687-9
9381178
Mol Cell. 2005 Feb 4;17(3):393-403
15694340
Genome Res. 2007 Oct;17(10):1537-45
17785539
Bioinformatics. 2004 Dec 12;20(18):3553-64
15284098
Science. 2005 Mar 11;307(5715):1621-5
15761153
Bioinformatics. 2005 Dec 15;21(24):4348-55
16234317
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6
15608262
Adv Exp Med Biol. 2006;587:41-52
17163154
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7
16723010
J Comput Biol. 2000;7(3-4):601-20
11108481
J Biol Chem. 2001 Jun 1;276(22):19495-502
11278302
Bioinformatics. 2005 Jan 15;21(2):171-8
15308542
Bioinformatics. 2007 Jan 1;23(1):38-43
17077100
Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16875-80
12486219
BMC Bioinformatics. 2006 Jun 14;7:299
16774678
Cancer Res. 2002 May 15;62(10):2890-6
12019169
Biochem Biophys Res Commun. 1996 Sep 24;226(3):801-9
8831693
Bioinformatics. 2002 Nov;18(11):1454-61
12424116
Nat Rev Genet. 2006 Jan;7(1):55-65
16369572
Math Biosci. 2002 Mar;176(1):35-51
11867082
Nucleic Acids Res. 2003 Jan 1;31(1):374-8
12520026
J Cell Biol. 2001 Oct 29;155(3):415-26
11684708
Nucleic Acids Res. 1999 Jan 1;27(1):29-34
9847135
Mol Cell. 2005 Jun 10;18(6):637-50
15949439
Genetics. 2003 Oct;165(2):747-57
14573485
J Biol Chem. 2003 Sep 26;278(39):37413-8
12871937
Bioinformatics. 2004 Nov 22;20(17):3146-55
15231528
Cell. 2000 Jan 7;100(1):57-70
10647931
Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
11309499
Immunity. 1996 Apr;4(4):387-96
8612133
EMBO J. 1998 Apr 15;17(8):2215-23
9545235
Science. 1999 Oct 15;286(5439):531-7
10521349
IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):583-595
17975270
Bioinformatics. 2006 Oct 15;22(20):2500-6
16895928
J Biol Chem. 2003 Jul 25;278(30):28045-51
12732644
Genome Res. 2004 Jul;14(7):1324-32
15231748