A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

Adel F.M. Ibrahim; Peter E. Hedley; Linda Cardle; Warren Kruger; David F. Marshall; Gary J. Muehlbauer; Robbie Waugh

doi:10.1007/s10142-005-0135-4

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

Adel F.M. Ibrahim, Peter E. Hedley, Linda Cardle, Warren Kruger, David F. Marshall, Gary J. Muehlbauer, Robbie Waugh

Agronomy and Plant Genetics

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

33 Scopus citations

Abstract

A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.

Original language	English (US)
Pages (from-to)	163-174
Number of pages	12
Journal	Functional and Integrative Genomics
Volume	5
Issue number	3
DOIs	https://doi.org/10.1007/s10142-005-0135-4
State	Published - Jul 2005

Bibliographical note

Funding Information:
Acknowledgements This work was supported by the Food Standards Agency in the UK (GO2) and a BBSRC ISIS award and a McKnight Landgrant Professorship to Dr. Gary Muehlbauer. The HarvEST database was kindly provided by Drs. Tim Close and Steve Wanamaker, UCR. We thank Ilze Druka for advice on data analysis and Arnis Druka for useful discussions about this work.

Keywords

Barley
Microarray
SAGE
Transcriptome

Access

10.1007/s10142-005-0135-4

OpenUrl availability

Full text

Cite this

@article{eedca114ebdd44128e43f89ed61ed03d,

title = "A comparative analysis of transcript abundance using SAGE and Affymetrix arrays",

abstract = "A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of {"}genes{"} and these are discussed.",

keywords = "Barley, Microarray, SAGE, Transcriptome",

author = "Ibrahim, {Adel F.M.} and Hedley, {Peter E.} and Linda Cardle and Warren Kruger and Marshall, {David F.} and Muehlbauer, {Gary J.} and Robbie Waugh",

note = "Funding Information: Acknowledgements This work was supported by the Food Standards Agency in the UK (GO2) and a BBSRC ISIS award and a McKnight Landgrant Professorship to Dr. Gary Muehlbauer. The HarvEST database was kindly provided by Drs. Tim Close and Steve Wanamaker, UCR. We thank Ilze Druka for advice on data analysis and Arnis Druka for useful discussions about this work.",

year = "2005",

month = jul,

doi = "10.1007/s10142-005-0135-4",

language = "English (US)",

volume = "5",

pages = "163--174",

journal = "Functional and Integrative Genomics",

issn = "1438-793X",

publisher = "Springer Verlag",

number = "3",

}

TY - JOUR

T1 - A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

AU - Ibrahim, Adel F.M.

AU - Hedley, Peter E.

AU - Cardle, Linda

AU - Kruger, Warren

AU - Marshall, David F.

AU - Muehlbauer, Gary J.

AU - Waugh, Robbie

N1 - Funding Information: Acknowledgements This work was supported by the Food Standards Agency in the UK (GO2) and a BBSRC ISIS award and a McKnight Landgrant Professorship to Dr. Gary Muehlbauer. The HarvEST database was kindly provided by Drs. Tim Close and Steve Wanamaker, UCR. We thank Ilze Druka for advice on data analysis and Arnis Druka for useful discussions about this work.

PY - 2005/7

Y1 - 2005/7

N2 - A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.

AB - A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.

KW - Barley

KW - Microarray

KW - SAGE

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=20444449787&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=20444449787&partnerID=8YFLogxK

U2 - 10.1007/s10142-005-0135-4

DO - 10.1007/s10142-005-0135-4

M3 - Article

C2 - 15714318

AN - SCOPUS:20444449787

SN - 1438-793X

VL - 5

SP - 163

EP - 174

JO - Functional and Integrative Genomics

JF - Functional and Integrative Genomics

IS - 3

ER -

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

Other files and links

Fingerprint

Cite this