Biostatistics 4:249-264 (2003)
© 2003 Oxford University Press
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Department of Biostatistics, Johns Hopkins University, Baltimore MD 21205, USA rafa{at}jhu.edu
Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia
Gene Logic Inc., Berkeley, CA, USA
Gene Logic Inc., Gaithersburg, MD, USA
Gene Logic Inc., Gaithersburg, MD, USA
Gene Logic Inc., Gaithersburg, MD, USA
Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia. Department of Statistics, University of California at Berkeley
*To whom correspondence should be addressed
In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip® system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip® arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip® arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip® arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance–mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed PM values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. Mathijs, K. J. J. Brauers, D. G. J. Jennen, A. Boorsma, M. H. M. van Herwijnen, R. W. H. Gottschalk, J. C. S. Kleinjans, and J. H. M. van Delft Discrimination for Genotoxic and Nongenotoxic Carcinogens by Gene Expression Profiling in Primary Mouse Hepatocytes Improves with Exposure Time Toxicol. Sci., December 1, 2009; 112(2): 374 - 384. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I Arijs, K Li, G Toedter, R Quintens, L Van Lommel, K Van Steen, P Leemans, G De Hertogh, K Lemaire, M Ferrante, et al. Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis Gut, December 1, 2009; 58(12): 1612 - 1619. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. T. Sredni, S. Gadd, C.-C. Huang, N. Breslow, P. Grundy, D. M. Green, J. S. Dome, R. C. Shamberger, J. B. Beckwith, E. J. Perlman, et al. Subsets of Very Low Risk Wilms Tumor Show Distinctive Gene Expression, Histologic, and Clinical Features Clin. Cancer Res., November 15, 2009; 15(22): 6800 - 6809. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Li, W. Zhang, M. Wu, S. Zhu, C. Gao, L. Sun, R. Zhang, N. Qiao, H. Xue, Y. Hu, et al. Gene expression-based classification and regulatory networks of pediatric acute lymphoblastic leukemia Blood, November 12, 2009; 114(20): 4486 - 4493. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. N. Nurtdinov, M. O. Vasiliev, A. S. Ershova, I. S. Lossev, and A. S. Karyagina PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays Nucleic Acids Res., November 11, 2009; (2009) gkp969v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Korkola, J. Houldsworth, D. R. Feldman, A. B. Olshen, L.-X. Qin, S. Patil, V. E. Reuter, G. J. Bosl, and R.S.K. Chaganti Identification and Validation of a Gene Expression Signature That Predicts Outcome in Adult Men With Germ Cell Tumors J. Clin. Oncol., November 1, 2009; 27(31): 5240 - 5247. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. H. Chan and M. L. Privalsky Isoform-Specific Transcriptional Activity of Overlapping Target Genes that Respond to Thyroid Hormone Receptors {alpha}1 and {beta}1 Mol. Endocrinol., November 1, 2009; 23(11): 1758 - 1775. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. Archer, V. R. Mas, K. David, D. G. Maluf, K. Bornstein, and R. A. Fisher Identifying Genes for Establishing a Multigenic Test for Hepatocellular Carcinoma Surveillance in Hepatitis C Virus-Positive Cirrhotic Patients Cancer Epidemiol. Biomarkers Prev., November 1, 2009; 18(11): 2929 - 2932. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Carlson, C. McCulloch, A. Koganti, S. B. Goodwin, T. R. Sutter, and J. B. Silkworth Divergent Transcriptomic Responses to Aryl Hydrocarbon Receptor Agonists between Rat and Human Primary Hepatocytes Toxicol. Sci., November 1, 2009; 112(1): 257 - 272. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Monticone, E. Biollo, A. Fabiano, M. Fabbi, A. Daga, F. Romeo, M. Maffei, A. Melotti, W. Giaretti, G. Corte, et al. z-Leucinyl-Leucinyl-Norleucinal Induces Apoptosis of Human Glioblastoma Tumor-Initiating Cells by Proteasome Inhibition and Mitotic Arrest Response Mol. Cancer Res., November 1, 2009; 7(11): 1822 - 1834. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Pollard, M. Nitz, A. Baras, P. Williams, C. Moskaluk, and D. Theodorescu Genoproteomic Mining of Urothelial Cancer Suggests {gamma}-Glutamyl Hydrolase and Diazepam-Binding Inhibitor as Putative Urinary Markers of Outcome after Chemotherapy Am. J. Pathol., November 1, 2009; 175(5): 1824 - 1830. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Bannenberg, M. Martinez, M. J. Rodriguez, M. A. Lopez, I. Ponce de Leon, M. Hamberg, and C. Castresana Functional Analysis of {alpha}-DOX2, an Active {alpha}-Dioxygenase Critical for Normal Development in Tomato Plants Plant Physiology, November 1, 2009; 151(3): 1421 - 1432. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. R. Shockley, D. Witmer, S. L. Burgess-Herbert, B. Paigen, and G. A. Churchill Effects of atherogenic diet on hepatic gene expression across mouse strains Physiol Genomics, November 1, 2009; 39(3): 172 - 182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. C. Banduseela, J. Ochala, Y.-W. Chen, H. Goransson, H. Norman, P. Radell, L. I. Eriksson, E. P. Hoffman, and L. Larsson Gene expression and muscle fiber function in a porcine ICU model Physiol Genomics, November 1, 2009; 39(3): 141 - 159. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Turro, A. Lewin, A. Rose, M. J. Dallman, and S. Richardson MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays Nucleic Acids Res., October 23, 2009; (2009) gkp853v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Malcovati, M. G. Della Porta, D. Pietra, E. Boveri, A. Pellagatti, A. Galli, E. Travaglino, A. Brisci, E. Rumi, F. Passamonti, et al. Molecular and clinical features of refractory anemia with ringed sideroblasts associated with marked thrombocytosis Blood, October 22, 2009; 114(17): 3538 - 3545. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Marot, J.-L. Foulley, C.-D. Mayer, and F. Jaffrezic Moderated effect size and P-value combinations for microarray meta-analyses Bioinformatics, October 15, 2009; 25(20): 2692 - 2699. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. J. S. Baerends, J.-L. Qiu, S. Rasmussen, H. B. Nielsen, and A. Brandt Impaired Uptake and/or Utilization of Leucine by Saccharomyces cerevisiae Is Suppressed by the SPT15-300 Allele of the TATA-Binding Protein Gene Appl. Envir. Microbiol., October 1, 2009; 75(19): 6055 - 6061. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Bosse, A. Miqdad, D. Fournier, A. Pepin, P. Pibarot, and P. Mathieu Refining Molecular Pathways Leading to Calcific Aortic Valve Stenosis by Studying Gene Expression Profile of Normal and Calcified Stenotic Human Aortic Valves Circ Cardiovasc Genet, October 1, 2009; 2(5): 489 - 498. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Obayashi and K. Kinoshita Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression DNA Res, October 1, 2009; 16(5): 249 - 260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Ting, M. J. Cowley, S. L. Hoon, M. Guilhaus, M. J. Raftery, and R. Cavicchioli Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling Mol. Cell. Proteomics, October 1, 2009; 8(10): 2227 - 2242. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. B. Williams, D. Pang, B. Delgado, M. Kocherginsky, M. Tretiakova, T. Krausz, D. Pan, J. He, M. K. McClintock, and S. D. Conzen A Model of Gene-Environment Interaction Reveals Altered Mammary Gland Gene Expression and Increased Tumor Growth following Social Isolation Cancer Prevention Research, October 1, 2009; 2(10): 850 - 861. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Haferlach, C. Mecucci, S. Schnittger, A. Kohlmann, M. Mancini, A. Cuneo, N. Testoni, G. Rege-Cambrin, A. Santucci, M. Vignetti, et al. AML with mutated NPM1 carrying a normal or aberrant karyotype show overlapping biologic, pathologic, immunophenotypic, and prognostic features Blood, October 1, 2009; 114(14): 3024 - 3032. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Mani, S. Venkatasubrahmanyam, M. Sanyal, S. Levy, A. Butte, K. Weinberg, and T. Jahn Wiskott-Aldrich syndrome protein is an effector of Kit signaling Blood, October 1, 2009; 114(14): 2900 - 2908. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. J. Molyneaux, P. Arlotta, R. M. Fame, J. L. MacDonald, K. L. MacQuarrie, and J. D. Macklis Novel Subtype-Specific Genes Identify Distinct Subpopulations of Callosal Projection Neurons J. Neurosci., September 30, 2009; 29(39): 12343 - 12354. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Zuber, G. Centeno, S. Pradervand, S. Nikolaeva, L. Maquelin, L. Cardinaux, O. Bonny, and D. Firsov Molecular clock is involved in predictive circadian adjustment of renal function PNAS, September 22, 2009; 106(38): 16523 - 16528. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. C. Culhane and J. Quackenbush Confounding Effects in "A Six-Gene Signature Predicting Breast Cancer Lung Metastasis" Cancer Res., September 15, 2009; 69(18): 7480 - 7485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Antonescu, A. Yoshida, T. Guo, N.-E. Chang, L. Zhang, N. P. Agaram, L.-X. Qin, M. F. Brennan, S. Singer, and R. G. Maki KDR Activating Mutations in Human Angiosarcomas Are Sensitive to Specific Kinase Inhibitors Cancer Res., September 15, 2009; 69(18): 7175 - 7179. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. T. Judy and H. Ji TileProbe: modeling tiling array probe effects using publicly available data Bioinformatics, September 15, 2009; 25(18): 2369 - 2375. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Comabella, J. D. Lunemann, J. Rio, A. Sanchez, C. Lopez, E. Julia, M. Fernandez, L. Nonell, M. Camina-Tato, F. Deisenhammer, et al. A type I interferon signature in monocytes is associated with poor response to interferon-{beta} in multiple sclerosis Brain, September 9, 2009; (2009) awp228v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Del Duca, G. Wong, P. Trieu, D. Rodaros, A. Kouremenos, A. Tadevosyan, G. Vaniotis, L. R. Villeneuve, C. I. Tchervenkov, S. Nattel, et al. Association of neonatal hypoxia with lasting changes in left ventricular gene expression: An animal model J. Thorac. Cardiovasc. Surg., September 1, 2009; 138(3): 538 - 546. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. MORAL, C. SEGRELLES, A. B. MARTINEZ-CRUZ, C. LORZ, M. SANTOS, R. GARCIA-ESCUDERO, J. LU, A. BUITRAGO, C. COSTA, C. SAIZ, et al. Transgenic Mice Expressing Constitutively Active Akt in Oral Epithelium Validate KLFA as a Potential Biomarker of Head and Neck Squamous Cell Carcinoma In Vivo, September 1, 2009; 23(5): 653 - 660. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Gaidatzis, K. Jacobeit, E. J. Oakeley, and M. B. Stadler Overestimation of alternative splicing caused by variable probe characteristics in exon arrays Nucleic Acids Res., September 1, 2009; 37(16): e107 - e107. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Frank, E. Pressman, R. Ophir, L. Althan, R. Shaked, M. Freedman, S. Shen, and N. Firon Transcriptional profiling of maturing tomato (Solanum lycopersicum L.) microspores reveals the involvement of heat shock proteins, ROS scavengers, hormones, and sugars in the heat stress response J. Exp. Bot., September 1, 2009; 60(13): 3891 - 3908. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Martinelli, S. L. Uratsu, R. L. Reagan, Y. Chen, D. Tricoli, O. Fiehn, D. M. Rocke, C. S. Gasser, and A. M. Dandekar Gene regulation in parthenocarpic tomato fruit J. Exp. Bot., September 1, 2009; 60(13): 3873 - 3890. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. J. White, C. Cheng, D. Sangare, N. F. Lobo, F. H. Collins, and N. J. Besansky The Population Genomics of Trans-Specific Inversion Polymorphisms in Anopheles gambiae Genetics, September 1, 2009; 183(1): 275 - 288. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-W. Lee, M. Efetova, J. C Engelmann, R. Kramell, C. Wasternack, J. Ludwig-Muller, R. Hedrich, and R. Deeken Agrobacterium tumefaciens Promotes Tumor Induction by Modulating Pathogen Defense in Arabidopsis thaliana PLANT CELL, September 1, 2009; 21(9): 2948 - 2962. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Albinsky, M. Kusano, M. Higuchi, N. Hayashi, M. Kobayashi, A. Fukushima, M. Mori, T. Ichikawa, K. Matsui, H. Kuroda, et al. Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism Mol Plant, August 26, 2009; (2009) ssp069v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Miller, K. Schlauch, R. Tam, D. Cortes, M. A. Torres, V. Shulaev, J. L. Dangl, and R. Mittler The Plant NADPH Oxidase RBOHD Mediates Rapid Systemic Signaling in Response to Diverse Stimuli Sci. Signal., August 18, 2009; 2(84): ra45 - ra45. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Patino-Garcia, M. Zalacain, C. Folio, C. Zandueta, L. Sierrasesumaga, M. San Julian, G. Toledo, J. De Las Rivas, and F. Lecanda Profiling of Chemonaive Osteosarcoma and Paired-Normal Cells Identifies EBF2 as a Mediator of Osteoprotegerin Inhibition to Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand-Induced Apoptosis Clin. Cancer Res., August 15, 2009; 15(16): 5082 - 5091. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Camateros, C. Kanagaratham, J. Henri, R. Sladek, T. J. Hudson, and D. Radzioch Modulation of the allergic asthma transcriptome following resiquimod treatment Physiol Genomics, August 7, 2009; 38(3): 303 - 318. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Pappas, G. Coppola, P. A. Gabatto, F. Gao, D. H. Geschwind, J. R. Oksenberg, and S. E. Baranzini Longitudinal system-based analysis of transcriptional responses to type I interferons Physiol Genomics, August 7, 2009; 38(3): 362 - 371. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. S. Collison, Z. Maqbool, S. M. Saleh, A. Inglis, N. J. Makhoul, R. Bakheet, M. Al-Johi, R. Al-Rabiah, M. Z. Zaidi, and F. A. Al-Mohanna Effect of dietary monosodium glutamate on trans fat-induced nonalcoholic fatty liver disease J. Lipid Res., August 1, 2009; 50(8): 1521 - 1537. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Chen, G. Lin, J. S. Huo, D. Barney, Z. Wang, T. Livshiz, D. J. States, Z. S. Qin, and J. Schwartz Computational and Functional Analysis of Growth Hormone (GH)-Regulated Genes Identifies the Transcriptional Repressor B-Cell Lymphoma 6 (Bc16) as a Participant in GH-Regulated Transcription Endocrinology, August 1, 2009; 150(8): 3645 - 3654. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. B. MARTINEZ-CRUZ, M. SANTOS, R. GARCIA-ESCUDERO, M. MORAL, C. SEGRELLES, C. LORZ, C. SAIZ, A. BUITRAGO-PEREZ, C. COSTA, and J. M. PARAMIO Spontaneous Tumor Formation in Trp53-deficient Epidermis Mediated by Chromosomal Instability and Inflammation Anticancer Res, August 1, 2009; 29(8): 3035 - 3042. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Guo, M. Baum, S. Grando, S. Ceccarelli, G. Bai, R. Li, M. von Korff, R. K. Varshney, A. Graner, and J. Valkoun Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage J. Exp. Bot., August 1, 2009; 60(12): 3531 - 3544. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Matzkin and T. A. Markow Transcriptional Regulation of Metabolism Associated With the Increased Desiccation Resistance of the Cactophilic Drosophila mojavensis Genetics, August 1, 2009; 182(4): 1279 - 1288. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Pesaresi, A. Hertle, M. Pribil, T. Kleine, R. Wagner, H. Strissel, A. Ihnatowicz, V. Bonardi, M. Scharfenberg, A. Schneider, et al. Arabidopsis STN7 Kinase Provides a Link between Short- and Long-Term Photosynthetic Acclimation PLANT CELL, August 1, 2009; 21(8): 2402 - 2423. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Volodarsky, N. Leviatan, A. Otcheretianski, and R. Fluhr HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome Plant Physiology, August 1, 2009; 150(4): 1796 - 1805. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Hu, C. Wang, D. Ng, R. Clifford, H. H. Yang, Z.-Z. Tang, Q.-H. Wang, X.-Y. Han, C. Giffen, A. M. Goldstein, et al. Genomic Characterization of Esophageal Squamous Cell Carcinoma from a High-Risk Population in China Cancer Res., July 15, 2009; 69(14): 5908 - 5917. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Maruyama, Y. Nakamichi, T. Itoh, B. Mikami, W. Hashimoto, and K. Murata Substrate Specificity of Streptococcal Unsaturated Glucuronyl Hydrolases for Sulfated Glycosaminoglycan J. Biol. Chem., July 3, 2009; 284(27): 18059 - 18069. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. G. Dorsey, C. C. Leitch, C. L. Renn, S. Lessans, B. A. Smith, X. M. Wang, and R. A. Dionne Genome-Wide Screen Identifies Drug-Induced Regulation of the Gene Giant Axonal Neuropathy (Gan) in a Mouse Model of Antiretroviral-Induced Painful Peripheral Neuropathy Biol Res Nurs, July 1, 2009; 11(1): 7 - 16. [Abstract] [PDF]
|
|
|
|
 |
|
 R. Singhal, K. Shankar, T. M Badger, and M. J Ronis Hepatic gene expression following consumption of soy protein isolate in female Sprague-Dawley rats differs from that produced by 17{beta}-estradiol treatment J. Endocrinol., July 1, 2009; 202(1): 141 - 152. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Song, V. Di Giovanni, N. He, K. Wang, A. Ingram, N. D. Rosenblum, and Y. Pei Systems biology of autosomal dominant polycystic kidney disease (ADPKD): computational identification of gene expression pathways and integrated regulatory networks Hum. Mol. Genet., July 1, 2009; 18(13): 2328 - 2343. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. K. Piper, N. N. Jonsson, C. Gondro, A. E. Lew-Tabor, P. Moolhuijzen, M. E. Vance, and L. A. Jackson Immunological Profiles of Bos taurus and Bos indicus Cattle Infested with the Cattle Tick, Rhipicephalus (Boophilus) microplus Clin. Vaccine Immunol., July 1, 2009; 16(7): 1074 - 1086. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Hardin and J. Wilson A note on oligonucleotide expression values not being normally distributed Biostat., July 1, 2009; 10(3): 446 - 450. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Mitsuda and M. Ohme-Takagi Functional Analysis of Transcription Factors in Arabidopsis Plant Cell Physiol., July 1, 2009; 50(7): 1232 - 1248. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Cantu, B. Blanco-Ulate, L. Yang, J. M. Labavitch, A. B. Bennett, and A. L.T. Powell Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene Plant Physiology, July 1, 2009; 150(3): 1434 - 1449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Vanden Wymelenberg, J. Gaskell, M. Mozuch, P. Kersten, G. Sabat, D. Martinez, and D. Cullen Transcriptome and Secretome Analyses of Phanerochaete chrysosporium Reveal Complex Patterns of Gene Expression Appl. Envir. Microbiol., June 15, 2009; 75(12): 4058 - 4068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Medvedovic, R. Gear, J. M. Freudenberg, J. Schneider, R. Bornschein, M. Yan, M. J. Mistry, H. Hendrix, S. Karyala, D. Halbleib, et al. Influence of fatty acid diets on gene expression in rat mammary epithelial cells Physiol Genomics, June 10, 2009; 38(1): 80 - 88. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Krebs, S. Khan, J. W. MacDonald, M. Sorenson, and D. M. Robins Regulator of sex-limitation KRAB zinc finger proteins modulate sex-dependent and -independent liver metabolism Physiol Genomics, June 10, 2009; 38(1): 16 - 28. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Mathijs, A. S. Kienhuis, K. J. J. Brauers, D. G. J. Jennen, A. Lahoz, J. C. S. Kleinjans, and J. H. M. van Delft Assessing the Metabolic Competence of Sandwich-Cultured Mouse Primary Hepatocytes Drug Metab. Dispos., June 1, 2009; 37(6): 1305 - 1311. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Putt, S. Hannenhalli, Y. Lu, P. Haines, H. R. Chandrupatla, E. E. Morrisey, K. B. Margulies, and T. P. Cappola Evidence for Coregulation of Myocardial Gene Expression by MEF2 and NFAT in Human Heart Failure Circ Cardiovasc Genet, June 1, 2009; 2(3): 212 - 219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Wang, H. Tang, J. E. Bowers, and A. H. Paterson Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization Genome Res., June 1, 2009; 19(6): 1026 - 1032. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Beroukhim, J.-P. Brunet, A. Di Napoli, K. D. Mertz, A. Seeley, M. M. Pires, D. Linhart, R. A. Worrell, H. Moch, M. A. Rubin, et al. Patterns of Gene Expression and Copy-Number Alterations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney Cancer Res., June 1, 2009; 69(11): 4674 - 4681. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P Meier, J Antonov, R Zbinden, A Kuhn, S Zbinden, S Gloekler, M Delorenzi, R Jaggi, and C Seiler Non-invasive gene-expression-based detection of well-developed collateral function in individuals with and without coronary artery disease Heart, June 1, 2009; 95(11): 900 - 908. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Deng, S. K. Koya, Y. Kong, and V. H. Meller Coordinated Regulation of Heterochromatic Genes in Drosophila melanogaster Males Genetics, June 1, 2009; 182(2): 481 - 491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Pan Network-based multiple locus linkage analysis of expression traits Bioinformatics, June 1, 2009; 25(11): 1390 - 1396. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Vandepoele, M. Quimbaya, T. Casneuf, L. De Veylder, and Y. Van de Peer Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks Plant Physiology, June 1, 2009; 150(2): 535 - 546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Aluru, J. Zola, A. Foudree, and S. R. Rodermel Chloroplast Photooxidation-Induced Transcriptome Reprogramming in Arabidopsis immutans White Leaf Sectors Plant Physiology, June 1, 2009; 150(2): 904 - 923. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. D. Crouser, D. A. Culver, K. S. Knox, M. W. Julian, G. Shao, S. Abraham, S. Liyanarachchi, J. E. Macre, M. D. Wewers, M. A. Gavrilin, et al. Gene Expression Profiling Identifies MMP-12 and ADAMDEC1 as Potential Pathogenic Mediators of Pulmonary Sarcoidosis Am. J. Respir. Crit. Care Med., May 15, 2009; 179(10): 929 - 938. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. V. Fournier, J. E. Fata, K. J. Martin, P. Yaswen, and M. J. Bissell Interaction of E-cadherin and PTEN Regulates Morphogenesis and Growth Arrest in Human Mammary Epithelial Cells Cancer Res., May 15, 2009; 69(10): 4545 - 4552. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Saito, A. Furuno, J. Sakurai, A. Sakamoto, H.-R. Park, K. Shin-ya, T. Tsuruo, and A. Tomida Chemical Genomics Identifies the Unfolded Protein Response as a Target for Selective Cancer Cell Killing during Glucose Deprivation Cancer Res., May 15, 2009; 69(10): 4225 - 4234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Jayaswal, M. Lutherborrow, D. D. F. Ma, and Y. Hwa Yang Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data Nucleic Acids Res., May 1, 2009; 37(8): e60 - e60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-S. Lee, C.-H. Chen, C.-N. Tsai, C.-L. Tsai, A. Chao, and T.-H. Wang Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips Nucleic Acids Res., May 1, 2009; 37(8): e61 - e61. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. B. Langdon, G. J. G. Upton, and A. P. Harrison Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips Brief Bioinform, May 1, 2009; 10(3): 259 - 277. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Bower, H. B. Gordon-Raagas, and M. A. Mulvey Conditioning of Uropathogenic Escherichia coli for Enhanced Colonization of Host Infect. Immun., May 1, 2009; 77(5): 2104 - 2112. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Van Vaerenbergh, L. Van Lommel, V. Ghislain, P. In't Veld, F. Schuit, H. M. Fatemi, P. Devroey, and C. Bourgain In GnRH antagonist/rec-FSH stimulated cycles, advanced endometrial maturation on the day of oocyte retrieval correlates with altered gene expression Hum. Reprod., May 1, 2009; 24(5): 1085 - 1091. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Yan, S. Deng, A. Metzger, U. Godtel-Armbrust, A. C.G. Porter, and L. Wojnowski Topoisomerase II{alpha}-dependent and -independent apoptotic effects of dexrazoxane and doxorubicin Mol. Cancer Ther., May 1, 2009; 8(5): 1075 - 1085. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Fukushima, M. Kusano, N. Nakamichi, M. Kobayashi, N. Hayashi, H. Sakakibara, T. Mizuno, and K. Saito Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination PNAS, April 28, 2009; 106(17): 7251 - 7256. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. S. Longo, P. L. Lugar, S. Yavuz, W. Zhang, P. H. L. Krijger, D. E. Russ, D. D. Jima, S. S. Dave, A. C. Grammer, and P. E. Lipsky Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting Blood, April 16, 2009; 113(16): 3706 - 3715. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Taylor, N. C. Berchtold, V. M. Perreau, C. H. Tu, N. Li Jeon, and C. W. Cotman Axonal mRNA in Uninjured and Regenerating Cortical Mammalian Axons J. Neurosci., April 15, 2009; 29(15): 4697 - 4707. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Getnet, C. H. Maris, E. L. Hipkiss, J. F. Grosso, T. J. Harris, H.-R. Yen, T. C. Bruno, S. Wada, A. Adler, R. W. Georgantas, et al. Tumor Recognition and Self-Recognition Induce Distinct Transcriptional Profiles in Antigen-Specific CD4 T Cells J. Immunol., April 15, 2009; 182(8): 4675 - 4685. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. C. Daniel, L. Marchionni, J. S. Hierman, J. T. Rhodes, W. L. Devereux, C. M. Rudin, R. Yung, G. Parmigiani, M. Dorsch, C. D. Peacock, et al. A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro Cancer Res., April 15, 2009; 69(8): 3364 - 3373. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Tornavaca, G. Pascual, M.L. Barreiro, M.T. Grande, A. Carretero, M. Riera, E. Garcia-Arumi, B. Bardaji, M. Gonzalez-Nunez, M.A. Montero, et al. Kidney Androgen-Regulated Protein Transgenic Mice Show Hypertension and Renal Alterations Mediated by Oxidative Stress Circulation, April 14, 2009; 119(14): 1908 - 1917. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Marotta, C. Ruiz-Roig, Y. Sarria, J. L. Peiro, F. Nunez, J. Ceron, F. Munell, and M. Roig-Quilis Muscle genome-wide expression profiling during disease evolution in mdx mice Physiol Genomics, April 10, 2009; 37(2): 119 - 132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schupp, A. G. Cristancho, M. I. Lefterova, E. A. Hanniman, E. R. Briggs, D. J. Steger, M. Qatanani, J. C. Curtin, J. Schug, S. A. Ochsner, et al. Re-expression of GATA2 Cooperates with Peroxisome Proliferator-activated Receptor-{gamma} Depletion to Revert the Adipocyte Phenotype J. Biol. Chem., April 3, 2009; 284(14): 9458 - 9464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Carrera, G. Rodrigo, and A. Jaramillo Model-based redesign of global transcription regulation Nucleic Acids Res., April 1, 2009; 37(5): e38 - e38. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Panagiotou, M. R. Andersen, T. Grotkjaer, T. B. Regueira, J. Nielsen, and L. Olsson Studies of the Production of Fungal Polyketides in Aspergillus nidulans by Using Systems Biology Tools Appl. Envir. Microbiol., April 1, 2009; 75(7): 2212 - 2220. [Abstract] [Full Text] [PDF]
|
|