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

Jun Lu; Anita Lal; Barry Merriman; Stan Nelson; Gregory Riggins

doi:10.1016/j.ygeno.2004.06.014

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

Jun Lu, Anita Lal, Barry Merriman, Stan Nelson, Gregory Riggins

School of Medicine

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

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.

Original language	English (US)
Pages (from-to)	631-636
Number of pages	6
Journal	Genomics
Volume	84
Issue number	4
DOIs	https://doi.org/10.1016/j.ygeno.2004.06.014
State	Published - Oct 2004

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2004.06.014

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title = "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.",

author = "Jun Lu and Anita Lal and Barry Merriman and Stan Nelson and Gregory Riggins",

note = "Funding Information: Support for this project was from the Duke University Genome Institute, the Cancer Genome Anatomy Project (NCI Contract S98-146), The Director's Challenge (NIH U01 CA88128), the Ludwig Trust, and the Irving J. Sherman Research Professorship in Neurosurgery (to G.J.R.).",

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AU - Lal, Anita

AU - Merriman, Barry

AU - Nelson, Stan

AU - Riggins, Gregory

N1 - Funding Information: Support for this project was from the Duke University Genome Institute, the Cancer Genome Anatomy Project (NCI Contract S98-146), The Director's Challenge (NIH U01 CA88128), the Ludwig Trust, and the Irving J. Sherman Research Professorship in Neurosurgery (to G.J.R.).

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

Abstract

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