ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data

被引:27
作者
van Wieringen, Wessel N.
Belien, Jeroen A. M.
Vosse, Sjoerd J.
Achame, Eskeatnaf M.
Ylstra, Bauke
机构
[1] VU Med Ctr, Dept Pathol, NL-1007 MB Amsterdam, Netherlands
[2] Vrije Univ Amsterdam, Dept Math, NL-1081 HV Amsterdam, Netherlands
关键词
D O I
10.1093/bioinformatics/btl269
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We describe a tool, called ACE-it ( Array CGH Expression integration tool). ACE-it links the chromosomal position of the gene dosage measured by array CGH to the genes measured by the expression array. ACE-it uses this link to statistically test whether gene dosage affects RNA expression.
引用
收藏
页码:1919 / 1920
页数:2
相关论文
共 9 条
[1]   Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene [J].
Albertson, DG ;
Ylstra, B ;
Segraves, R ;
Collins, C ;
Dairkee, SH ;
Kowbel, D ;
Kuo, WL ;
Gray, JW ;
Pinkel, D .
NATURE GENETICS, 2000, 25 (02) :144-146
[2]   CGH-Plotter: MATLAB toolbox for CGH-data analysis [J].
Autio, R ;
Hautaniemi, S ;
Kauraniemi, P ;
Yli-Harja, O ;
Astola, J ;
Wolf, M ;
Kallioniemi, A .
BIOINFORMATICS, 2003, 19 (13) :1714-1715
[3]   CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].
BENJAMINI, Y ;
HOCHBERG, Y .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300
[4]   Breakpoint identification and smoothing of array comparative genomic hybridization data [J].
Jong, K ;
Marchiori, E ;
Meijer, G ;
Van der Vaart, A ;
Ylstra, B .
BIOINFORMATICS, 2004, 20 (18) :3636-3637
[5]   Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma [J].
Nigro, JM ;
Misra, A ;
Zhang, L ;
Smirnov, I ;
Colman, H ;
Griffin, C ;
Ozburn, N ;
Chen, MG ;
Pan, E ;
Koul, D ;
Yung, WKA ;
Feuerstein, BG ;
Aldape, KD .
CANCER RESEARCH, 2005, 65 (05) :1678-1686
[6]   Circular binary segmentation for the analysis of array-based DNA copy number data [J].
Olshen, AB ;
Venkatraman, ES ;
Lucito, R ;
Wigler, M .
BIOSTATISTICS, 2004, 5 (04) :557-572
[7]   Array comparative genomic hybridization and its applications in cancer [J].
Pinkel, D ;
Albertson, DG .
NATURE GENETICS, 2005, 37 (Suppl 6) :S11-S17
[8]   Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors [J].
Pollack, JR ;
Sorlie, T ;
Perou, CM ;
Rees, CA ;
Jeffrey, SS ;
Lonning, PE ;
Tibshirani, R ;
Botstein, D ;
Borresen-Dale, AL ;
Brown, PO .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (20) :12963-12968
[9]   BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH) [J].
Ylstra, B ;
van den IJssel, P ;
Carvalho, B ;
Brakenhoff, RH ;
Meijer, GA .
NUCLEIC ACIDS RESEARCH, 2006, 34 (02) :445-450