Statistical methods for gene set co-expression analysis.
BACKGROUND
The power of a microarray experiment derives from the identification of genes differentially regulated across biological conditions. To date, differential regulation is most often taken to mean differential expression, and a number of useful methods for identifying differentially expressed (DE) genes or gene sets are available. However, such methods are not able to identify many relevant classes of differentially regulated genes. One important example concerns differentially co-expressed (DC) genes.


RESULTS
We propose an approach, gene set co-expression analysis (GSCA), to identify DC gene sets. The GSCA approach provides a false discovery rate controlled list of interesting gene sets, does not require that genes be highly correlated in at least one biological condition and is readily applied to data from individual or multiple experiments, as we demonstrate using data from studies of lung cancer and diabetes.


BACKGROUND
The GSCA approach is implemented in R and available at www.biostat.wisc.edu/ approximately kendzior/GSCA/.


BACKGROUND
kendzior@biostat.wisc.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Choi
YounJeong
Y
Department of Statistics, University of Wisconsin - Madison, Madison, WI 53706, USA.
Kendziorski
Christina
C
D019295:Computational Biology / Q000379:methods*; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis
Development. 2000 Jun;127(12):2617-27
10821760
Cancer Res. 2002 Aug 1;62(15):4427-33
12154050
Bioinformatics. 2005 Dec 15;21(24):4348-55
16234317
Br J Cancer. 1998;77(2):270-6
9460998
Nat Genet. 2000 May;25(1):25-9
10802651
Bioinformatics. 2005 Mar;21(6):754-64
15479708
Nat Rev Genet. 2006 Jan;7(1):55-65
16369572
Genome Biol. 2004;5(10):R80
15461798
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
12883005
Genome Res. 2008 May;18(5):706-16
18347327
Biochem Biophys Res Commun. 1995 Aug 24;213(3):789-95
7654239
J Immunol. 2008 Mar 1;180(5):3313-8
18292556
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13790-5
11707567
Methods Mol Biol. 2007;408:171-91
18314583
Cancer Genet Cytogenet. 2006 Aug;169(1):39-44
16875935
Cancer Res. 2007 Oct 1;67(19):9117-24
17909016
PLoS Genet. 2005 Sep;1(3):e39
16470937
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17973-8
17101986
Physiol Genomics. 2004 Feb 13;16(3):361-70
14645736
Nat Rev Cancer. 2008 Jan;8(1):51-6
18046334
Bioinformatics. 2007 Jan 15;23(2):257-8
17098774
Cancer Inform. 2007 Feb 14;2:87-97
19458761
BMC Bioinformatics. 2006 Nov 20;7:509
17116249
BMC Genomics. 2005 Apr 27;6:59
15854232
Cancer Res. 1998 Oct 15;58(20):4660-6
9788619
Nat Med. 2006 Sep;12(9):1048-55
16906154
Br J Cancer. 2007 Dec 17;97(12):1648-54
18043580
Diabetes. 2003 Jan;52(1):1-8
12502486
Cancer Biol Ther. 2008 Oct;7(10):1619-27
19018165
Bioinformatics. 2003;19 Suppl 1:i84-90
12855442
Clin Cancer Res. 2004 May 1;10(9):2922-7
15131026
Bioinformatics. 2005 May 1;21(9):1943-9
15647293
Nat Genet. 1995 Mar;9(3):249-55
7773287
Am J Pathol. 2007 Sep;171(3):1047-57
17724140
Nat Med. 2002 Aug;8(8):816-24
12118244
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
16199517
J Endocrinol. 2000 Apr;165(1):67-77
10750037
Hum Mutat. 1999;14(1):67-70
10447260
Diabetes. 2008 Sep;57(9):2272-9
18519799
Bioinformatics. 2004 Nov 22;20(17):3146-55
15231528
Cancer. 1958 Mar-Apr;11(2):351-6
13511356
Bioinformatics. 2008 Apr 1;24(7):889-96
18263644
J Immunol. 2008 May 15;180(10):6962-9
18453618
Am J Dermatopathol. 2003 Feb;25(1):21-7
12544095
J Clin Invest. 2005 May;115(5):1111-9
15864338
Diabetes. 2006 Aug;55(8):2311-7
16873695
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
10592173
J Comput Biol. 2001;8(1):37-52
11339905
Cancer Biol Ther. 2007 Dec;6(12):1858-66
18087215
Bioinformatics. 2007 Nov 1;23(21):2903-9
17921496
Bioinformatics. 2004 Aug 4;20 Suppl 1:i194-9
15262799
PLoS Comput Biol. 2006 Jul 21;2(7):e89
16854212
Bioinformatics. 2009 Jan 15;25(2):211-7
19038984
Int J Cancer. 2001 Oct 15;94(2):237-42
11668504
Endocrinology. 2002 Nov;143(11):4437-46
12399441
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13784-9
11707590
Bioinformatics. 2007 Nov 15;23(22):3032-8
17893087
Oncogene. 1998 Oct 1;17(13):1749-53
9796705
Eur J Immunol. 2001 Feb;31(2):323-32
11180095
Genome Res. 2002 Feb;12(2):244-54
11827944