Rat toxicogenomic study reveals analytical consistency across microarray platforms.
To validate and extend the findings of the MicroArray Quality Control (MAQC) project, a biologically relevant toxicogenomics data set was generated using 36 RNA samples from rats treated with three chemicals (aristolochic acid, riddelliine and comfrey) and each sample was hybridized to four microarray platforms. The MAQC project assessed concordance in intersite and cross-platform comparisons and the impact of gene selection methods on the reproducibility of profiling data in terms of differentially expressed genes using distinct reference RNA samples. The real-world toxicogenomic data set reported here showed high concordance in intersite and cross-platform comparisons. Further, gene lists generated by fold-change ranking were more reproducible than those obtained by t-test P value or Significance Analysis of Microarrays. Finally, gene lists generated by fold-change ranking with a nonstringent P-value cutoff showed increased consistency in Gene Ontology terms and pathways, and hence the biological impact of chemical exposure could be reliably deduced from all platforms analyzed.
Guo
Lei
L
National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.
Lobenhofer
Edward K
EK
Wang
Charles
C
Shippy
Richard
R
Harris
Stephen C
SC
Zhang
Lu
L
Mei
Nan
N
Chen
Tao
T
Herman
Damir
D
Goodsaid
Federico M
FM
Hurban
Patrick
P
Phillips
Kenneth L
KL
Xu
Jun
J
Deng
Xutao
X
Sun
Yongming Andrew
YA
Tong
Weida
W
Dragan
Yvonne P
YP
Shi
Leming
L
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D011785:Quality Assurance, Health Care / Q000379:methods*; D011786:Quality Control; D051381:Rats; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D043922:Toxicogenetics / Q000379:methods*