Development of a spot reliability evaluation score for DNA microarrays.
We developed a reliability index named SRED (Spot Reliability Evaluation Score for DNA microarrays) that represents the probability that the calibrated gene expression level from a DNA microarray would be less than a factor of 2 different from that of quantitative real-time polymerase chain reaction assays whose dynamic quantification range is treated statistically to be similar to that of the DNA microarray. To define the SRED score, two parameters, the reproducibility of measurement value and the relative expression value were selected from nine candidate parameters. The SRED score supplies the probability that the expression level in each spot of a microarray is less than a certain-fold different compared to other expression profiling data, such as QRT-PCR. This score was applied to approximately 1,500,000 points of the expression profile in the RIKEN Expression Array Database.
Matsumura
Yonehiro
Y
Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Shimokawa
Kazuro
K
Hayashizaki
Yoshihide
Y
Ikeo
Kazuho
K
Tateno
Yoshio
Y
Kawai
Jun
J
D000465:Algorithms; D000818:Animals; D001921:Brain / Q000378:metabolism; D045744:Cell Line, Tumor; D002531:Cerebellum / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics; D004622:Embryo, Mammalian / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D051542:Hepatocyte Nuclear Factor 3-beta; D051379:Mice; D008810:Mice, Inbred C57BL; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods / Q000592:standards; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics; D014162:Transfection
D004268:DNA-Binding Proteins; C496503:Foxa2 protein, mouse; D009687:Nuclear Proteins; D014157:Transcription Factors; D051542:Hepatocyte Nuclear Factor 3-beta; D012313:RNA