Báo cáo y học: "Correction: A DNA microarray survey of gene expression in normal human tissues" pdf

Genome Biology 2005, 6:404 Correction Correction: 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 †§ and Jonathan R Pollack* Addresses: *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. ¶ Current address: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 80544, USA. Correspondence: Patrick O Brown. Email: pbrown@cmgm.stanford.edu. Jonathan R Pollack. Email: pollack1@stanford.edu Published: 19 August 2005 Genome Biology 2005, 6:404 (doi:10.1186/gb-2005-6-9-404) The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/9/404 © 2005 BioMed Central Ltd Received: 22 July 2005 Accepted: 29 July 2005 We wish to report two corrections to our study [1], neither of which alters the interpretation of the data or the conclu- sions 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, indicat- ing 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. Additional data files Additional data file 2 contains a corrected list of the variably expressed genes. References 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. comment reviews reports deposited research interactions information refereed research (See the corrected figure on the next page) 404.2 Genome Biology 2005, Volume 6, Issue 9, Article 404 Shyamsundar et al. http://genomebiology.com/2005/6/9/404 Genome Biology 2005, 6:404 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. Esophagus 0022 Esophagus 0406 Esophagus 0331 Placenta 2876 Vagina 0304 Cervix 2209 Cervix 2385 Lung 1356 Lung 0221 Lung 1351 Lung 0330 Ovary 0408 Fallopian tube 065B Fallopian tube 065A Fallopian tube 2184 Fallopian tube 2386 Ovary 0466 Ovary 0314 Ovary 0538 Ovary 1080 Cervix, endo cervical canal 1200 Uterine corpus, myometriun 1205 Uterus, endomyometrium 0002 Uterus, endomyometrium 0126 Uterus, endomyometrium 0158 Uterus, endomyometrium 002B Small bowel, duodenum 0825 Bladder 1678 Bladder 1004 Seminal vesicle 0233 Seminal vesicle 0234 Seminal vesicle 0235 Prostate 1277 Prostate 0845 Prostate 0805 Prostate 0782 Prostate 1045 Breast, lactating 0162 Salivary gland, parotid 0506 Salivary gland, parotid 0493 Salivary gland, parotid 0396 Salivary gland, parotid 1762 Epididymus 2125 Parathyroid 2995 Parathyroid 1748 Parathyroid 0499 Thyroid 0838 Thyroid 1193 Thyroid 3077 Thyroid 0182 Thyroid 0029 Testes 1853 Testes 1068 Testes 0553 Brain, temporal cortex 2272 Brain, occipital cortex 2271 Brain, frontal cortex 2271 Brain, frontal cortex 2272 Brain, occipital cortex 2273 Brain, occipital cortex 2272 Brain, temporal cortex 2273 Brain, frontal cortex 2273 Adrenal 0433 Adrenal 1111 Adrenal 1354 Thyroid 0555 Adrenal 0558 Heart 0559 Pericardium 0465 Muscle, abdominal 0031 Diaphragm 0366 Muscle, right calf 0315 Heart 0980 Heart 0477 Heart 2869 Heart 0841 Heart 0024 Gallbladder 2131 Stomach, fundus 0878 Colon, ascending 0222 Stomach, body 0468 Stomach, body 0328 Stomach, pylorus 2173 Small bowel, ileum 0359 Small bowel, duodenum 2174 Colon, sigmoid 0361 Colon 2075 Kidney 0265 Kidney 1651 Kidney 1594 Kidney 0226 Kidney 0088 Liver 0560 Liver 1274 Liver 1267 Liver 0032 Liver 0586 Pancreas 2650 Pancreas 0432 Thymus 0512 Tonsil 1398 Lymph node 1337 Lymph node 0599 Lymph node, axillary 0936 Lymph node, axillary 1187 Tonsil 1428 Tonsil 3011 Tonsil 2852 Thymus 0035 Buffycoat 3643 Buffycoat 3642 Spleen 0405 Spleen 0089 Spleen 0125 Lymph node 2096 (a) (b) 2 4 >8 0.5 0.25 < 0.125 1 (c) TTRAP ABCC4 NKX3-1 AA229499 PAK1IP1 TRIP8 AA425692 AMD1 AI078552 AMD1 AA229573 RDH11 RDH11 STEAP2 KIAA1411 AA772497 FLJ13409 PRIM2A MSH2 ACLY TTRAP ABCC4 NKX3-1 AA229499 PAK1IP1 TRIP8 AA425692 AMD1 AI078552 AMD1 AA229573 RDH11 RDH11 STEAP2 KIAA1411 AA772497 FLJ13409 PRIM2A MSH2 ACLY -20 -15 -10 -5 0 5 10 15 -15 -10 -5 0 5 10 15 Prostate mRNA vs Genomic DNA Calculated Prostate mRNA vs Genomic DNA R = 0.93 . 0235 Prostate 1277 Prostate 0845 Prostate 0805 Prostate 0782 Prostate 1045 Breast, lactating 0162 Salivary gland, parotid 0506 Salivary gland, parotid 0493 Salivary gland, parotid 0396 Salivary gland,. 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. 0.125 1 (c) TTRAP ABCC4 NKX3-1 AA229499 PAK1IP1 TRIP8 AA425692 AMD1 AI078552 AMD1 AA229573 RDH11 RDH11 STEAP2 KIAA1411 AA772497 FLJ13409 PRIM 2A MSH2 ACLY TTRAP ABCC4 NKX3-1 AA229499 PAK1IP1 TRIP8 AA425692 AMD1 AI078552 AMD1 AA229573 RDH11 RDH11 STEAP2 KIAA1411 AA772497 FLJ13409 PRIM 2A MSH2 ACLY -20 -15 -10 -5 0 5 10 15 -15