gb-2005-6-9-404 GBJ Correction <p>Correction: A DNA microarray survey of gene expression in normal human tissues</p> Shyamsundar Radha Kim H Young Higgins P John Montgomery Kelli Jorden Michelle Sethuraman Anand van de Rijn Matt Botstein David Brown O Patrick pbrown@cmgm.stanford.edu Pollack R Jonathan pollack1@stanford.edu

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

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

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

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

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

 Genome Biology 1465-6906 2005 6 9 404 http://genomebiology.com/2005/6/9/404 10.1186/gb-2005-6-9-404 19 8 2005 2005 BioMed Central Ltd

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

A correction to A DNA microarray survey of gene expression in normal human tissues by R Shyamsundar, YH Kim, JP Higgins, K Montgomery, M Jorden, A Sethuraman, M van de Rijn, D Botstein, PO Brown and JR Pollack. Genome Biology 2005, 6:R22

 Genome studies Methods Medicine Cancer

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.

<p>Figure 4</p>

Estimating relative transcript abundance

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.

<p>Additional data file 2</p>

A table listing the variably expressed genes

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)

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 <p>A DNA microarray survey of gene expression in normal human tissues.</p> Shyamsundar R Kim YH Higgins JP Montgomery K Jorden M Sethuraman A van de Rijn M Botstein D Brown PO Pollack JR Genome Biol 2005 6 R22 1088941 15774023 10.1186/gb-2005-6-3-r22