Functional & Integrative Genomics

, Volume 5, Issue 3, pp 163–174 | Cite as

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
Original Paper


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.


Barley Transcriptome SAGE Microarray 



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.

Supplementary material

Supplementary table 1A Whole caryopsis top 100 SAGE tags

s10142_2005_135_table_1a.pdf (278 kb)
(PDF 278 KB)

Supplementary table 1B Embryo top 100 SAGE tags

s10142_2005_135_table_1b.pdf (171 kb)
(PDF 171 KB)

Supplementary table 2A Whole caryopsis top 100 GeneChip scores

s10142_2005_135_table_2a.pdf (141 kb)
(PDF 141 KB)

Supplementary table 2B Embryo top 100 GeneChip scores

s10142_2005_135_table_2b.pdf (150 kb)
(PDF 151 KB)

Supplementary table 3

s10142_2005_135_table_3.xls (76 kb)
(Excel 76 KB)

Supplementary table 4

s10142_2005_135_table_4.xls (61 kb)
(Excel 61 KB)

Supplementary table 5

s10142_2005_135_table_5.xls (49 kb)
(Excel 49 KB)

Supplementary table 6 Differential expression in barley whole caryopsis and embryo detected by SAGE and GeneChip Analysis

s10142_2005_135_table_6.pdf (93 kb)
(PDF 94 KB)

Supplementary table 7

s10142_2005_135_table_7.xls (32 kb)
(Excel 32 KB)


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Adel F. M. Ibrahim
    • 1
  • Peter E. Hedley
    • 2
  • Linda Cardle
    • 3
  • Warren Kruger
    • 4
  • David F. Marshall
    • 3
  • Gary J. Muehlbauer
    • 4
  • Robbie Waugh
    • 1
  1. 1.Genome DynamicsScottish Crop Research InstituteDundeeUK
  2. 2.Gene ExpressionScottish Crop Research InstituteDundeeUK
  3. 3.Computational BiologyScottish Crop Research InstituteDundeeUK
  4. 4.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA

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