A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips

Genomics. 2004 Oct;84(4):631-6. doi: 10.1016/j.ygeno.2004.06.014.

Abstract

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA, Complementary / analysis
  • Expressed Sequence Tags*
  • Gene Expression Profiling*
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • RNA, Messenger / genetics*
  • Transcription, Genetic*

Substances

  • DNA, Complementary
  • RNA, Messenger