A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips.
A comparison study of short SAGE versus GeneChip and long SAGE was conducted to determine if data were interchangeable between the techniques. Although SAGE and Affymetrix chip expression levels showed a significant correlation using the set of genes for which there was reliable and unambiguous mapping from tag-to-gene identification, correlation coefficients were low (0.51 for the Spearman's correlation coefficient with p < 0.0001). A quantitative analysis comparing the use of 10-bp SAGE tags to 17-bp SAGE tags indicated that the short SAGE technology was more efficient at identifying differentially expressed tags. However, 4-7% of the 10-bp tags were redundancies that could have been resolved by long SAGE and 10-20% of the short SAGE tags had no obvious match to currently annotated human transcript sequences.
Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA.
Jun
J
Lu
Anita
A
Lal
Barry
B
Merriman
Stan
S
Nelson
Gregory
G
Riggins
D018076:DNA, Complementary / Q000032:analysis; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic
D018076:DNA, Complementary; D012333:RNA, Messenger