Genome Biology

, 6:404 | Cite as

Erratum to: A DNA microarray survey of gene expression in normal human tissues

  • Radha Shyamsundar
  • Young H Kim
  • John P Higgins
  • Kelli Montgomery
  • Michelle Jorden
  • Anand Sethuraman
  • Matt van de Rijn
  • David Botstein
  • Patrick O Brown
  • Jonathan R Pollack
Erratum
We wish to report two corrections to our study [1], neither of which alters the interpretation of the data or the conclusions drawn. First, we have discovered that the data file from a microarray hybridization (prostate RNA versus normal genomic DNA) used to derive the plot in Figure 4a became corrupted during data processing. The corrected plot (Figure 4a) displays a stronger correlation between directly and indirectly estimated transcript levels, indicating even better performance of our method of estimating transcript abundance. The corrected data file has been deposited to the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) repositories. Second, we have identified a 'frame-shift' in the Additional data file 2 (Sheet 5) data set; the corrected data file has been deposited to the supplemental site.
Figure 4

Estimating relative transcript abundance. (a) Comparison of transcript levels estimated either directly by hybridization of prostate sample mRNA versus normal female genomic DNA, or indirectly by multiplying the ratio of prostate sample mRNA versus common reference mRNA by the ratio of common reference mRNA versus normal female genomic DNA. The correlation value (R) is indicated. (b) Prostate-specific gene expression cluster, extracted from the hierarchical cluster shown in Figure 1a, displayed as mean-centered relative gene expression (ratio-fold change scale indicated). (c) The same gene expression feature as in (b), now displayed as transcript abundance (relative to the average transcript level for all expressed genes), calculated indirectly using the common reference mRNA versus normal female genomic DNA hybridization data.

Additional data files

Additional data file 2 contains a corrected list of the variably expressed genes.

Supplementary material

13059_2005_1034_MOESM1_ESM.zip (24.1 mb)
Additional data file 2: A table listing the variably expressed genes. Sheet 1: Dataset represented in Figure 1, which includes well-measured genes in ≥75% of samples, and with ≥4-fold ratio variation from the mean in at least 2 samples; samples ordered by clustering. Sheet 2: Variably expressed genes which are well-measured in ≥75% of samples, with ≥2-fold ratio variation from the mean in at least 2 samples; samples ordered by anatomic site. Sheet 3: Variably expressed genes which are well-measured in ≥25% of samples, with ≥4-fold ratio variation from the mean in at least 2 samples; samples ordered by anatomic site. Sheet 4: Same dataset as sheet 1, but here ratios represent relative transcript abundance (See Materials and methods). Sheet 5: Same dataset as sheet 2, but here ratios represent relative transcript abundance (See Materials and methods). Sheet 6: Same dataset as sheet 3, but here ratios represent relative transcript abundance (See Materials and methods) (ZIP 24 MB)
13059_2005_1034_MOESM2_ESM.eps (5.4 mb)
Authors’ original file for figure 1

References

  1. 1.
    Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR: A DNA microarray survey of gene expression in normal human tissues. Genome Biol. 2005, 6: R22-10.1186/gb-2005-6-3-r22.PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© BioMed Central Ltd 2005

Authors and Affiliations

  • Radha Shyamsundar
    • 1
    • 2
  • Young H Kim
    • 1
  • John P Higgins
    • 1
  • Kelli Montgomery
    • 1
  • Michelle Jorden
    • 1
  • Anand Sethuraman
    • 3
  • Matt van de Rijn
    • 1
    • 2
  • David Botstein
    • 3
    • 5
  • Patrick O Brown
    • 2
    • 4
  • Jonathan R Pollack
    • 1
  1. 1.Department of PathologyStanford UniversityStanfordUSA
  2. 2.Department of BiochemistryStanford UniversityStanfordUSA
  3. 3.Department of GeneticsStanford UniversityStanfordUSA
  4. 4.Howard Hughes Medical Institute, Stanford UniversityStanfordUSA
  5. 5.Lewis-Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonUSA

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