Nucleic Acids Research, 2003, Vol. 31, No. 4 e15
© 2003 Oxford University Press
Summaries of Affymetrix GeneChip probe level data
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA, 1 Biostatistics Group, University of California, Berkeley, CA, USA, 2 Gene Logic Inc., Berkeley, CA, USA, 3 Mathematical Sciences Department, Johns Hopkins University, Baltimore, MD, USA, 4 Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia and 5 Department of Statistics, University of California, Berkeley, CA, USA
*To whom correspondence should be addressed. Tel: +1 410 614 5157; Fax: +1 410 955 0958; Email: rafa{at}jhu.edu
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11–20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. J van Dijk, E. J. Feskens, M. B Bos, D. W. Hoelen, R. Heijligenberg, M. G. Bromhaar, L. C. de Groot, J. H. de Vries, M. Muller, and L. A Afman A saturated fatty acid-rich diet induces an obesity-linked proinflammatory gene expression profile in adipose tissue of subjects at risk of metabolic syndrome Am. J. Clinical Nutrition, December 1, 2009; 90(6): 1656 - 1664. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Aparicio, E. Carnero, X. Abad, N. Razquin, E. Guruceaga, V. Segura, and P. Fortes Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair Nucleic Acids Res., November 19, 2009; (2009) gkp1028v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Garbarino, M. Padamsee, L. Wilcox, P. M. Oelkers, D. D'Ambrosio, K. V. Ruggles, N. Ramsey, O. Jabado, A. Turkish, and S. L. Sturley Sterol and Diacylglycerol Acyltransferase Deficiency Triggers Fatty Acid-mediated Cell Death J. Biol. Chem., November 6, 2009; 284(45): 30994 - 31005. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. S. Yang, W. W. Xu, M. Tesfaye, J. F. S. Lamb, H.-J. G. Jung, D. A. Samac, C. P. Vance, and J. W. Gronwald Single-Feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa The Plant Genome, November 1, 2009; 2(3): 224 - 232. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Meyer, M. Arentshorst, S. J. Flitter, B. M. Nitsche, M. J. Kwon, C. G. Reynaga-Pena, S. Bartnicki-Garcia, C. A. M. J. J. van den Hondel, and A. F. J. Ram Reconstruction of Signaling Networks Regulating Fungal Morphogenesis by Transcriptomics Eukaryot. Cell, November 1, 2009; 8(11): 1677 - 1691. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. R. Nayak, M. Kearns, R. S. Spielman, and V. G. Cheung Coexpression network based on natural variation in human gene expression reveals gene interactions and functions Genome Res., November 1, 2009; 19(11): 1953 - 1962. [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]
|
|
|
|
 |
|
 Y. Pang, J. P. Wenger, K. Saathoff, G. J. Peel, J. Wen, D. Huhman, S. N. Allen, Y. Tang, X. Cheng, M. Tadege, et al. A WD40 Repeat Protein from Medicago truncatula Is Necessary for Tissue-Specific Anthocyanin and Proanthocyanidin Biosynthesis But Not for Trichome Development Plant Physiology, November 1, 2009; 151(3): 1114 - 1129. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ge, M. Wei, P. Fabrizio, J. Hu, C. Cheng, V. D. Longo, and L. M. Li Comparative analyses of time-course gene expression profiles of the long-lived sch9{Delta} mutant Nucleic Acids Res., October 30, 2009; (2009) gkp849v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Giannakis, H. K. Backhed, S. L. Chen, J. J. Faith, M. Wu, J. L. Guruge, L. Engstrand, and J. I. Gordon Response of Gastric Epithelial Progenitors to Helicobacter pylori Isolates Obtained from Swedish Patients with Chronic Atrophic Gastritis J. Biol. Chem., October 30, 2009; 284(44): 30383 - 30394. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Horng, G. Kreiman, C. Ellsworth, D. Page, M. Blank, K. Millen, and M. Sur Differential Gene Expression in the Developing Lateral Geniculate Nucleus and Medial Geniculate Nucleus Reveals Novel Roles for Zic4 and Foxp2 in Visual and Auditory Pathway Development J. Neurosci., October 28, 2009; 29(43): 13672 - 13683. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Gersten, M. Alirezaei, M. C. G. Marcondes, C. Flynn, T. Ravasi, T. Ideker, and H. S. Fox An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction J. Neurosci., October 7, 2009; 29(40): 12467 - 12476. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Andrei and C. Kendziorski An efficient method for identifying statistical interactors in gene association networks Biostat., October 1, 2009; 10(4): 706 - 718. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. S. Balakumaran, A. Porrello, D. S. Hsu, W. Glover, A. Foye, J. Y. Leung, B. A. Sullivan, W. C. Hahn, M. Loda, and P. G. Febbo MYC Activity Mitigates Response to Rapamycin in Prostate Cancer through Eukaryotic Initiation Factor 4E-Binding Protein 1-Mediated Inhibition of Autophagy Cancer Res., October 1, 2009; 69(19): 7803 - 7810. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. J. M. de Jonge, E. S. J. M. de Bont, P. J. M. Valk, J. J. Schuringa, M. Kies, C. M. Woolthuis, R. Delwel, N. J. G. M. Veeger, E. Vellenga, B. Lowenberg, et al. AML at older age: age-related gene expression profiles reveal a paradoxical down-regulation of p16INK4A mRNA with prognostic significance Blood, October 1, 2009; 114(14): 2869 - 2877. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. W. Hong, S. M. Hong, J. W. Yoo, Y. C. Lee, S. Kim, J. T. Lis, and D.-k. Lee Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome PNAS, August 25, 2009; 106(34): 14276 - 14280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Chen, I. Cuevas, P. A. Kenny, H. Miyake, K. Mace, C. Ghajar, A. Boudreau, M. Bissell, and N. Boudreau Endothelial Cell Migration and Vascular Endothelial Growth Factor Expression Are the Result of Loss of Breast Tissue Polarity Cancer Res., August 15, 2009; 69(16): 6721 - 6729. [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]
|
|
|
|
|
|
S. Bicciato, R. Spinelli, M. Zampieri, E. Mangano, F. Ferrari, L. Beltrame, I. Cifola, C. Peano, A. Solari, and C. Battaglia A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets Nucleic Acids Res., August 1, 2009; 37(15): 5057 - 5070. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Walsh, H. Yi, J. Friedman, K.-i. Cho, N. Tserentsoodol, S. McKinnon, K. Searle, A. Yeh, and P. A. Ferreira Gene and Protein Expression Pilot Profiling and Biomarkers in an Experimental Mouse Model of Hypertensive Glaucoma Experimental Biology and Medicine, August 1, 2009; 234(8): 918 - 930. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X.-Y. Wang, A. Demelash, H. Kim, S. Jensen-Taubman, E. H. Dakir, L. Ozbun, M. J. Birrer, and R. I. Linnoila Matrilysin-1 Mediates Bronchiolization of Alveoli, a Potential Premalignant Change in Lung Cancer Am. J. Pathol., August 1, 2009; 175(2): 592 - 604. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. K. Yadav, J. J. Renfrow, D. M. Scholtens, H. Xie, G. E. Duran, C. Bredel, H. Vogel, J. P. Chandler, A. Chakravarti, P. A. Robe, et al. Monosomy of Chromosome 10 Associated With Dysregulation of Epidermal Growth Factor Signaling in Glioblastomas JAMA, July 15, 2009; 302(3): 276 - 289. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Langer, G. Marcucci, K. B. Holland, M. D. Radmacher, K. Maharry, P. Paschka, S. P. Whitman, K. Mrozek, C. D. Baldus, R. Vij, et al. Prognostic Importance of MN1 Transcript Levels, and Biologic Insights From MN1-Associated Gene and MicroRNA Expression Signatures in Cytogenetically Normal Acute Myeloid Leukemia: A Cancer and Leukemia Group B Study J. Clin. Oncol., July 1, 2009; 27(19): 3198 - 3204. [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]
|
|
|
|
 |
|
 C. Cheng, K. Shen, C. Song, J. Luo, and G. C. Tseng Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction Bioinformatics, July 1, 2009; 25(13): 1655 - 1661. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. D. Pfister, W. C. Reinhold, K. Agama, S. Gupta, S. A. Khin, R. J. Kinders, R. E. Parchment, J. E. Tomaszewski, J. H. Doroshow, and Y. Pommier Topoisomerase I levels in the NCI-60 cancer cell line panel determined by validated ELISA and microarray analysis and correlation with indenoisoquinoline sensitivity Mol. Cancer Ther., July 1, 2009; 8(7): 1878 - 1884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-J. Oh, Y. S. Kim, C.-W. Kwon, H. K. Park, J. S. Jeong, and J.-K. Kim Overexpression of the Transcription Factor AP37 in Rice Improves Grain Yield under Drought Conditions Plant Physiology, July 1, 2009; 150(3): 1368 - 1379. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Mantelli, L. Schaffer, R. Dana, S. R. Head, and P. Argueso Glycogene Expression in Conjunctiva of Patients with Dry Eye: Downregulation of Notch Signaling Invest. Ophthalmol. Vis. Sci., June 1, 2009; 50(6): 2666 - 2672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Tsuchiya, M. Oku, Y. Imanaka, R. Kunimoto, Y. Okuno, K. Terasawa, F. Sato, G. Tsujimoto, and K. Shimizu MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells Nucleic Acids Res., June 1, 2009; 37(11): 3821 - 3827. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Geeleher, D. Morris, J. P. Hinde, and A. Golden BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server Bioinformatics, June 1, 2009; 25(11): 1438 - 1439. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yu, R. McDaid, J. Lee, P. Possik, L. Li, S. M. Kumar, D. E. Elder, P. Van Belle, P. Gimotty, M. Guerra, et al. The Role of BRAF Mutation and p53 Inactivation during Transformation of a Subpopulation of Primary Human Melanocytes Am. J. Pathol., June 1, 2009; 174(6): 2367 - 2377. [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]
|
|
|
|
 |
|
 H. Zhu, G.-J. Li, L. Ding, X. Cui, H. Berg, S. M. Assmann, and Y. Xia Arabidopsis Extra Large G-Protein 2 (XLG2) Interacts with the G{beta} Subunit of Heterotrimeric G Protein and Functions in Disease Resistance Mol Plant, May 1, 2009; 2(3): 513 - 525. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. I. Lee, W. K. Lee, J. H. Shin, B. K. Han, S. Moon, S. Cho, T. Park, H. Kim, and J. Y. Han Sexually dimorphic gene expression in the chick brain before gonadal differentiation Poult. Sci., May 1, 2009; 88(5): 1003 - 1015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-T. Tai, E. Soydan, W. Song, M. Fulciniti, K. Kim, F. Hong, X.-F. Li, P. Burger, M. J. Rumizen, S. Nahar, et al. CS1 promotes multiple myeloma cell adhesion, clonogenic growth, and tumorigenicity via c-maf-mediated interactions with bone marrow stromal cells Blood, April 30, 2009; 113(18): 4309 - 4318. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Mendiratta, E. Mostaghel, J. Guinney, A. K. Tewari, A. Porrello, W. T. Barry, P. S. Nelson, and P. G. Febbo Genomic Strategy for Targeting Therapy in Castration-Resistant Prostate Cancer J. Clin. Oncol., April 20, 2009; 27(12): 2022 - 2029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. A. Johnson, M. Boyle, A. Bashashati, S. Leach, A. Brooks-Wilson, L. H. Sehn, M. Chhanabhai, R. R. Brinkman, J. M. Connors, A. P. Weng, et al. Diffuse large B-cell lymphoma: reduced CD20 expression is associated with an inferior survival Blood, April 16, 2009; 113(16): 3773 - 3780. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. van der Veen, J. M. Oliveira, W. A. M. van den Berg, and L. H. de Graaff Analysis of Variance Components Reveals the Contribution of Sample Processing to Transcript Variation Appl. Envir. Microbiol., April 15, 2009; 75(8): 2414 - 2422. [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]
|
|
|
|
 |
|
 S. P. Gong, H. Kim, E. J. Lee, S. T. Lee, S. Moon, H.-J. Lee, and J. M. Lim Change in gene expression of mouse embryonic stem cells derived from parthenogenetic activation Hum. Reprod., April 1, 2009; 24(4): 805 - 814. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. H. Kim, Y. S. Kim, S.-H. Park, Y. J. Koo, Y. D. Choi, Y.-Y. Chung, I.-J. Lee, and J.-K. Kim Methyl Jasmonate Reduces Grain Yield by Mediating Stress Signals to Alter Spikelet Development in Rice Plant Physiology, April 1, 2009; 149(4): 1751 - 1760. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Lippold, D. H. Sanchez, M. Musialak, A. Schlereth, W.-R. Scheible, D. K. Hincha, and M. K. Udvardi AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis Plant Physiology, April 1, 2009; 149(4): 1761 - 1772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F.-X. Hubert, S. A. Kinkel, P. E. Crewther, P. Z. F. Cannon, K. E. Webster, M. Link, R. Uibo, M. K. O'Bryan, A. Meager, S. P. Forehan, et al. Aire-Deficient C57BL/6 Mice Mimicking the Common Human 13-Base Pair Deletion Mutation Present with Only a Mild Autoimmune Phenotype J. Immunol., March 15, 2009; 182(6): 3902 - 3918. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. de Reynies, G. Assie, D. S. Rickman, F. Tissier, L. Groussin, F. Rene-Corail, B. Dousset, X. Bertagna, E. Clauser, and J. Bertherat Gene Expression Profiling Reveals a New Classification of Adrenocortical Tumors and Identifies Molecular Predictors of Malignancy and Survival J. Clin. Oncol., March 1, 2009; 27(7): 1108 - 1115. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Hernandez, A. E. Rodriguez, M. Gonzalez, R. Benito, C. Fontanillo, V. Sandoval, M. Romero, G. Martin-Nunez, A. G. de Coca, R. Fisac, et al. A high number of losses in 13q14 chromosome band is associated with a worse outcome and biological differences in patients with B-cell chronic lymphoid leukemia Haematologica, March 1, 2009; 94(3): 364 - 371. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Tauris, S. Borg, P. L. Gregersen, and P. B. Holm A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling J. Exp. Bot., March 1, 2009; 60(4): 1333 - 1347. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Chandran, Y. C. Tai, G. Hather, J. Dewdney, C. Denoux, D. G. Burgess, F. M. Ausubel, T. P. Speed, and M. C. Wildermuth Temporal Global Expression Data Reveal Known and Novel Salicylate-Impacted Processes and Regulators Mediating Powdery Mildew Growth and Reproduction on Arabidopsis Plant Physiology, March 1, 2009; 149(3): 1435 - 1451. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Perugorria, J. Castillo, M. U. Latasa, S. Goni, V. Segura, B. Sangro, J. Prieto, M. A. Avila, and C. Berasain Wilms' Tumor 1 Gene Expression in Hepatocellular Carcinoma Promotes Cell Dedifferentiation and Resistance to Chemotherapy Cancer Res., February 15, 2009; 69(4): 1358 - 1367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Besnard, S. E. Wert, M. T. Stahlman, A. D. Postle, Y. Xu, M. Ikegami, and J. A. Whitsett Deletion of Scap in Alveolar Type II Cells Influences Lung Lipid Homeostasis and Identifies a Compensatory Role for Pulmonary Lipofibroblasts J. Biol. Chem., February 6, 2009; 284(6): 4018 - 4030. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Burchard, A. L. Jackson, V. Malkov, R. H.V. Needham, Y. Tan, S. R. Bartz, H. Dai, A. B. Sachs, and P. S. Linsley MicroRNA-like off-target transcript regulation by siRNAs is species specific RNA, February 1, 2009; 15(2): 308 - 315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Fischer, K. L. Goss, T. E. Scheetz, C. L. Wohlford-Lenane, J. M. Snyder, and P. B. McCray Jr. Differential Gene Expression in Human Conducting Airway Surface Epithelia and Submucosal Glands Am. J. Respir. Cell Mol. Biol., February 1, 2009; 40(2): 189 - 199. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Mariappan, J. Winkler, S. Chen, H. Schulz, J. Hescheler, and A. Sachinidis Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells. Genes Cells, February 1, 2009; 14(2): 243 - 260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Dienz, S. M. Eaton, J. P. Bond, W. Neveu, D. Moquin, R. Noubade, E. M. Briso, C. Charland, W. J. Leonard, G. Ciliberto, et al. The induction of antibody production by IL-6 is indirectly mediated by IL-21 produced by CD4+ T cells J. Exp. Med., January 16, 2009; 206(1): 69 - 78. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Kaur, I. B. Lansky, and A. Wilks The Role of the Cytoplasmic Heme-binding Protein (PhuS) of Pseudomonas aeruginosa in Intracellular Heme Trafficking and Iron Homeostasis J. Biol. Chem., January 2, 2009; 284(1): 56 - 66. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. G. Hodgson, R.-F. Yeh, A. Ray, N. J. Wang, I. Smirnov, M. Yu, S. Hariono, J. Silber, H. S. Feiler, J. W. Gray, et al. Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts Neuro-oncol, January 1, 2009; 11(5): 477 - 487. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S.N. Seshasayee, G. M. Fraser, M. M. Babu, and N. M. Luscombe Principles of transcriptional regulation and evolution of the metabolic system in E. coli Genome Res., January 1, 2009; 19(1): 79 - 91. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Asare, Z. Gao, V. J. Carey, R. Wang, and V. Seyfert-Margolis Power enhancement via multivariate outlier testing with gene expression arrays Bioinformatics, January 1, 2009; 25(1): 48 - 53. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Marston, V. Weston, J. Jesson, E. Maina, C. McConville, A. Agathanggelou, A. Skowronska, K. Mapp, K. Sameith, J. E. Powell, et al. Stratification of pediatric ALL by in vitro cellular responses to DNA double-strand breaks provides insight into the molecular mechanisms underlying clinical response Blood, January 1, 2009; 113(1): 117 - 126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. N. Jorissen, L. Lipton, P. Gibbs, M. Chapman, J. Desai, I. T. Jones, T. J. Yeatman, P. East, I. P.M. Tomlinson, H. W. Verspaget, et al. DNA Copy-Number Alterations Underlie Gene Expression Differences between Microsatellite Stable and Unstable Colorectal Cancers Clin. Cancer Res., December 15, 2008; 14(24): 8061 - 8069. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Ota and H. Sasaki Mammalian Tead proteins regulate cell proliferation and contact inhibition as transcriptional mediators of Hippo signaling Development, December 15, 2008; 135(24): 4059 - 4069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Astapova, L. J. Lee, C. Morales, S. Tauber, M. Bilban, and A. N. Hollenberg The nuclear corepressor, NCoR, regulates thyroid hormone action in vivo PNAS, December 9, 2008; 105(49): 19544 - 19549. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. E. Nicolas, H. Pais, F. Schwach, M. Lindow, S. Kauppinen, V. Moulton, and T. Dalmay Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140 RNA, December 1, 2008; 14(12): 2513 - 2520. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Rodriguez-Caballero, A. C. Garcia-Montero, P. Barcena, J. Almeida, F. Ruiz-Cabello, M. D. Tabernero, P. Garrido, S. Munoz-Criado, Y. Sandberg, A. W. Langerak, et al. Expanded cells in monoclonal TCR-{alpha}{beta}+/CD4+/NKa+/CD8-/+dim T-LGL lymphocytosis recognize hCMV antigens Blood, December 1, 2008; 112(12): 4609 - 4616. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bye, M. A. Hoydal, D. Catalucci, M. Langaas, O. J. Kemi, V. Beisvag, L. G. Koch, S. L. Britton, O. Ellingsen, and U. Wisloff Gene expression profiling of skeletal muscle in exercise-trained and sedentary rats with inborn high and low VO2max Physiol Genomics, November 12, 2008; 35(3): 213 - 221. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Morris, C. W. Dawson, W. Wei, J. D. O'Neil, S. E. Stewart, J. Jia, A. I. Bell, L. S. Young, and J. R. Arrand Epstein-Barr virus-encoded LMP1 induces a hyperproliferative and inflammatory gene expression programme in cultured keratinocytes J. Gen. Virol., November 1, 2008; 89(11): 2806 - 2820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Li, P. Hao, S. Zheng, K. Tu, H. Fan, R. Zhu, G. Ding, C. Dong, C. Wang, X. Li, et al. Gene expression module-based chemical function similarity search Nucleic Acids Res., November 1, 2008; 36(20): e137 - e137. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Cosgrove, Y. Zhou, T. S. Gardner, and E. D. Kolaczyk Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia Bioinformatics, November 1, 2008; 24(21): 2482 - 2490. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bye, M. Langaas, M. A. Hoydal, O. J. Kemi, G. Heinrich, L. G. Koch, S. L. Britton, S. M. Najjar, O. Ellingsen, and U. Wisloff Aerobic capacity-dependent differences in cardiac gene expression Physiol Genomics, October 8, 2008; 33(1): 100 - 109. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. H. Jakobsen, G. L. Storvold, H. Bremseth, T. Follestad, K. Sand, M. Mack, K. S. Olsen, A. G. Lundemo, J. G. Iversen, H. E. Krokan, et al. DHA induces ER stress and growth arrest in human colon cancer cells: associations with cholesterol and calcium homeostasis J. Lipid Res., October 1, 2008; 49(10): 2089 - 2100. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. N. McCall and R. A. Irizarry Consolidated strategy for the analysis of microarray spike-in data Nucleic Acids Res., October 1, 2008; 36(17): e108 - e108. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. E. Andersen, H. J. Clewell III, E. Bermudez, G. A. Willson, and R. S. Thomas Genomic Signatures and Dose-Dependent Transitions in Nasal Epithelial Responses to Inhaled Formaldehyde in the Rat Toxicol. Sci., October 1, 2008; 105(2): 368 - 383. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Owzar, W. T. Barry, S.-H. Jung, I. Sohn, and S. L. George Statistical Challenges in Preprocessing in Microarray Experiments in Cancer Clin. Cancer Res., October 1, 2008; 14(19): 5959 - 5966. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Kisand, M. Link, A. S. B. Wolff, A. Meager, L. Tserel, T. Org, A. Murumagi, R. Uibo, N. Willcox, K. Trebusak Podkrajsek, et al. Interferon autoantibodies associated with AIRE deficiency decrease the expression of IFN-stimulated genes Blood, October 1, 2008; 112(7): 2657 - 2666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Brune, E. Tiacci, I. Pfeil, C. Doring, S. Eckerle, C. J.M. van Noesel, W. Klapper, B. Falini, A. von Heydebreck, D. Metzler, et al. Origin and pathogenesis of nodular lymphocyte-predominant Hodgkin lymphoma as revealed by global gene expression analysis J. Exp. Med., September 29, 2008; 205(10): 2251 - 2268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Rattner, L. Toulabi, J. Williams, H. Yu, and J. Nathans The Genomic Response of the Retinal Pigment Epithelium to Light Damage and Retinal Detachment J. Neurosci., September 24, 2008; 28(39): 9880 - 9889. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Pang, G. J. Peel, S. B. Sharma, Y. Tang, and R. A. Dixon A transcript profiling approach reveals an epicatechin-specific glucosyltransferase expressed in the seed coat of Medicago truncatula PNAS, September 16, 2008; 105(37): 14210 - 14215. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J Brennan, J. A Sharp, C. M Lefevre, and K. R Nicholas Uncoupling the mechanisms that facilitate cell survival in hormone-deprived bovine mammary explants J. Mol. Endocrinol., September 1, 2008; 41(3): 103 - 116. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Hu, L. Saba, K. Kechris, S. V. Bhave, P. L. Hoffman, and B. Tabakoff Genomic Insights into Acute Alcohol Tolerance J. Pharmacol. Exp. Ther., September 1, 2008; 326(3): 792 - 800. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Gabriely, T. Wurdinger, S. Kesari, C. C. Esau, J. Burchard, P. S. Linsley, and A. M. Krichevsky MicroRNA 21 Promotes Glioma Invasion by Targeting Matrix Metalloproteinase Regulators Mol. Cell. Biol., September 1, 2008; 28(17): 5369 - 5380. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Wiles, D. Ravi, S. Bhavani, and A. J.R. Bishop An Analysis of Normalization Methods for Drosophila RNAi Genomic Screens and Development of a Robust Validation Scheme J Biomol Screen, September 1, 2008; 13(8): 777 - 784. [Abstract] [PDF]
|
|
|
|
 |
|
 G. G. Fernandez-Ranvier, J. Weng, R.-F. Yeh, E. Khanafshar, I. Suh, C. Barker, Q. Y. Duh, O. H. Clark, and E. Kebebew Identification of Biomarkers of Adrenocortical Carcinoma Using Genomewide Gene Expression Profiling Arch Surg, September 1, 2008; 143(9): 841 - 846. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-L. Qiu, L. Zhou, B.-W. Yun, H. B. Nielsen, B. K. Fiil, K. Petersen, J. MacKinlay, G. J. Loake, J. Mundy, and P. C. Morris Arabidopsis Mitogen-Activated Protein Kinase Kinases MKK1 and MKK2 Have Overlapping Functions in Defense Signaling Mediated by MEKK1, MPK4, and MKS1 Plant Physiology, September 1, 2008; 148(1): 212 - 222. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-C. Corvol, D. Pelletier, R. G. Henry, S. J. Caillier, J. Wang, D. Pappas, S. Casazza, D. T. Okuda, S. L. Hauser, J. R. Oksenberg, et al. Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological event PNAS, August 19, 2008; 105(33): 11839 - 11844. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Y. Chiang, A. Villanueva, Y. Hoshida, J. Peix, P. Newell, B. Minguez, A. C. LeBlanc, D. J. Donovan, S. N. Thung, M. Sole, et al. Focal Gains of VEGFA and Molecular Classification of Hepatocellular Carcinoma Cancer Res., August 15, 2008; 68(16): 6779 - 6788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Klapper, M. Szczepanowski, B. Burkhardt, H. Berger, M. Rosolowski, S. Bentink, C. Schwaenen, S. Wessendorf, R. Spang, P. Moller, et al. Molecular profiling of pediatric mature B-cell lymphoma treated in population-based prospective clinical trials Blood, August 15, 2008; 112(4): 1374 - 1381. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. R.A. Ehrhardt, A. Hijikata, H. Kitamura, O. Ohara, J.-Y. Wang, and M. D. Cooper Discriminating gene expression profiles of memory B cell subpopulations J. Exp. Med., August 4, 2008; 205(8): 1807 - 1817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Wan, F. Luo, S. E. Wert, L. Zhang, Y. Xu, M. Ikegami, Y. Maeda, S. M. Bell, and J. A. Whitsett Kruppel-like factor 5 is required for perinatal lung morphogenesis and function Development, August 1, 2008; 135(15): 2563 - 2572. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-X. Li, Y. Oono, J. Zhu, X.-J. He, J.-M. Wu, K. Iida, X.-Y. Lu, X. Cui, H. Jin, and J.-K. Zhu The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance PLANT CELL, August 1, 2008; 20(8): 2238 - 2251. [Abstract] [Full Text] [PDF]
|
|