A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips
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.
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SAGE sampling depth of approximately 100,000 tags per library yields gene-detection sensitivity approximately equivalent to that of fluorescence-based microarray approaches.
“Our SAGE sampling depth (~100,000 tags per library) yields gene-detection sensitivity approximately equivalent to that of fluorescence-based microarray approaches [42]”
From A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE) (2007) · cites this paper as [42]
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References 16 · Cited by 55
- Authors
- Lu, J., Lal, A., Merriman, B., Nelson, S., & Riggins, G.
- Affiliations
- University of California, San Francisco (US)
- University of California, Los Angeles (US)
- Johns Hopkins University (US)
- Corresponding author
- Riggins, Gregory
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2004-10
- Volume
- 84
- Issue
- 4
- Pages
- 631-636
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W2072477416
- Cited by
- 55
- References
- 16
- Citations by year
- 2014: 1 · 2013: 1 · 2012: 4
- FWCI
- 3.09
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Genomics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Cancer Institute (U01CA088128, U01 CA88128)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Keywords
- suppression subtractive hybridization, oligonucleotide microarrays, Affymetrix GeneChip, gene expression profiling
- MeSH terms
- Humans, RNA, Messenger, Transcription, Genetic, DNA, Complementary, Expressed Sequence Tags, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling
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