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

Radha Shyamsundar¹^,2, Young H Kim¹, John P Higgins¹, Kelli Montgomery¹, Michelle Jorden¹, Anand Sethuraman³, Matt van de Rijn¹^,2, David Botstein³^,5, Patrick O Brown²^,4 and Jonathan R Pollack¹

¹Department of Pathology, Stanford University, Stanford, CA 94305, USA

²Department of Biochemistry, Stanford University, Stanford, CA 94305, USA

³Department of Genetics, Stanford University, Stanford, CA 94305, USA

⁴Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA

⁵Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 80544, USA

author email corresponding author email

Genome Biology 2005, 6:404doi:10.1186/gb-2005-6-9-404

Subject areas: Genome studies, Methods, Medicine, Cancer

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2005/6/9/404

Published:

19 August 2005

Correction

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

1 contains a corrected list of the variably expressed genes.

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)

Format: ZIP Size: 24.7MB Download file

References

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. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text

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

Correction

Additional data files

References

Have something to say? Post a comment on this article!