Spurious spatial periodicity of co-expression in microarray data due to printing design.
Global transcriptome data is increasingly combined with sophisticated mathematical analyses to extract information about the functional state of a cell. Yet the extent to which the results reflect experimental bias at the expense of true biological information remains largely unknown. Here we show that the spatial arrangement of probes on microarrays and the particulars of the printing procedure significantly affect the log-ratio data of mRNA expression levels measured during the Saccharomyces cerevisiae cell cycle. We present a numerical method that filters out these technology-derived contributions from the existing transcriptome data, leading to improved functional predictions. The example presented here underlines the need to routinely search and compensate for inherent experimental bias when analyzing systematically collected, internally consistent biological data sets.
Balázsi
Gábor
G
Department of Pathology, Feinberg School of Medicine, Northwestern University, Ward Building 6-204, 303 East Chicago Avenue, Chicago, IL 60611, USA. g-balazsi@northwestern.edu <g-balazsi@northwestern.edu>
Kay
Krin A
KA
Barabási
Albert-László
AL
Oltvai
Zoltán N
ZN
D002453:Cell Cycle; D016000:Cluster Analysis; D003198:Computer Simulation; D018076:DNA, Complementary; D020869:Gene Expression Profiling / Q000379:methods*; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010507:Periodicity; D012333:RNA, Messenger / Q000096:biosynthesis; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D015983:Selection Bias
D018076:DNA, Complementary; D012333:RNA, Messenger