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:
|
|
 |
|
  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]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 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., June 19, 2009; (2009) gkp520v1. [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]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 M. Gouti and A. Gavalas Hoxb1 Controls Cell Fate Specification and Proliferative Capacity of Neural Stem and Progenitor Cells Stem Cells, August 1, 2008; 26(8): 1985 - 1997. [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]
|
|
|
|
 |
|
 Z. H. Gumus, B. Du, A. Kacker, J. O. Boyle, J. M. Bocker, P. Mukherjee, K. Subbaramaiah, A. J. Dannenberg, and H. Weinstein Effects of Tobacco Smoke on Gene Expression and Cellular Pathways in a Cellular Model of Oral Leukoplakia Cancer Prevention Research, July 1, 2008; 1(2): 100 - 111. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. W.K. Ho, M. Stefani, C. G. dos Remedios, and M. A. Charleston Differential variability analysis of gene expression and its application to human diseases Bioinformatics, July 1, 2008; 24(13): i390 - i398. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R.N. Baumforth, A. Birgersdotter, G. M. Reynolds, W. Wei, G. Kapatai, J. R. Flavell, E. Kalk, K. Piper, S. Lee, L. Machado, et al. Expression of the Epstein-Barr Virus-Encoded Epstein-Barr Virus Nuclear Antigen 1 in Hodgkin's Lymphoma Cells Mediates Up-Regulation of CCL20 and the Migration of Regulatory T Cells Am. J. Pathol., July 1, 2008; 173(1): 195 - 204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. M. N. Dohmann, M. P. Levesque, E. Isono, M. Schmid, and C. Schwechheimer Auxin Responses in Mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 Signalosome Plant Physiology, July 1, 2008; 147(3): 1369 - 1379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Nairn, W. S. York, K. Harris, E. M. Hall, J. M. Pierce, and K. W. Moremen Regulation of Glycan Structures in Animal Tissues: TRANSCRIPT PROFILING OF GLYCAN-RELATED GENES J. Biol. Chem., June 20, 2008; 283(25): 17298 - 17313. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. I. Joensuu, W. M. Abdel-Rahman, M. Ollikainen, S. Ruosaari, S. Knuutila, and P. Peltomaki Epigenetic Signatures of Familial Cancer Are Characteristic of Tumor Type and Family Category Cancer Res., June 15, 2008; 68(12): 4597 - 4605. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. S. Roberts, R. S. Thomas, and D. C. Dorman Gene Expression Changes Following Acute Hydrogen Sulfide (H2S)-induced Nasal Respiratory Epithelial Injury Toxicol Pathol, June 1, 2008; 36(4): 560 - 567. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. T.-B. G. Schjoldager, H. R. Maltesen, S. Balmer, L. R. Lund, M. H. Claesson, H. Sjostrom, J. T. Troelsen, and J. Olsen Cellular cross talk in the small intestinal mucosa: postnatal lymphocytic immigration elicits a specific epithelial transcriptional response Am J Physiol Gastrointest Liver Physiol, June 1, 2008; 294(6): G1335 - G1343. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Mintz-Oron, T. Mandel, I. Rogachev, L. Feldberg, O. Lotan, M. Yativ, Z. Wang, R. Jetter, I. Venger, A. Adato, et al. Gene Expression and Metabolism in Tomato Fruit Surface Tissues Plant Physiology, June 1, 2008; 147(2): 823 - 851. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Langer, M. D. Radmacher, A. S. Ruppert, S. P. Whitman, P. Paschka, K. Mrozek, C. D. Baldus, T. Vukosavljevic, C.-G. Liu, M. E. Ross, et al. High BAALC expression associates with other molecular prognostic markers, poor outcome, and a distinct gene-expression signature in cytogenetically normal patients younger than 60 years with acute myeloid leukemia: a Cancer and Leukemia Group B (CALGB) study Blood, June 1, 2008; 111(11): 5371 - 5379. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. S. Chen-Plotkin, F. Geser, J. B. Plotkin, C. M. Clark, L. K. Kwong, W. Yuan, M. Grossman, V. M. Van Deerlin, J. Q. Trojanowski, and V. M.-Y. Lee Variations in the progranulin gene affect global gene expression in frontotemporal lobar degeneration Hum. Mol. Genet., May 15, 2008; 17(10): 1349 - 1362. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Garcia, M. M. Ihrig, R. C. Fry, Y. Feng, S. Xu, S. R. Boutin, A. B. Rogers, S. Muthupalani, L. D. Samson, and J. G. Fox Genetic Susceptibility to Chronic Hepatitis Is Inherited Codominantly in Helicobacter hepaticus-Infected AB6F1 and B6AF1 Hybrid Male Mice, and Progression to Hepatocellular Carcinoma Is Linked to Hepatic Expression of Lipogenic Genes and Immune Function-Associated Networks Infect. Immun., May 1, 2008; 76(5): 1866 - 1876. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Chalkley, Y. M. Moshkin, K. Langenberg, K. Bezstarosti, A. Blastyak, H. Gyurkovics, J. A. A. Demmers, and C. P. Verrijzer The Transcriptional Coactivator SAYP Is a Trithorax Group Signature Subunit of the PBAP Chromatin Remodeling Complex Mol. Cell. Biol., May 1, 2008; 28(9): 2920 - 2929. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Pierce, R. D. Unwin, C. A. Evans, S. Griffiths, L. Carney, L. Zhang, E. Jaworska, C.-F. Lee, D. Blinco, M. J. Okoniewski, et al. Eight-channel iTRAQ Enables Comparison of the Activity of Six Leukemogenic Tyrosine Kinases Mol. Cell. Proteomics, May 1, 2008; 7(5): 853 - 863. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Pachot, M.-A. Cazalis, F. Venet, F. Turrel, C. Faudot, N. Voirin, J. Diasparra, N. Bourgoin, F. Poitevin, B. Mougin, et al. Decreased Expression of the Fractalkine Receptor CX3CR1 on Circulating Monocytes as New Feature of Sepsis-Induced Immunosuppression J. Immunol., May 1, 2008; 180(9): 6421 - 6429. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Shabalin, H. Tjelmeland, C. Fan, C. M. Perou, and A. B. Nobel Merging two gene-expression studies via cross-platform normalization Bioinformatics, May 1, 2008; 24(9): 1154 - 1160. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Horan, C. Jang, J. Bailey-Serres, R. Mittler, C. Shelton, J. F. Harper, J.-K. Zhu, J. C. Cushman, M. Gollery, and T. Girke Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis Plant Physiology, May 1, 2008; 147(1): 41 - 57. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Stoecklin, S. A. Tenenbaum, T. Mayo, S. V. Chittur, A. D. George, T. E. Baroni, P. J. Blackshear, and P. Anderson Genome-wide Analysis Identifies Interleukin-10 mRNA as Target of Tristetraprolin J. Biol. Chem., April 25, 2008; 283(17): 11689 - 11699. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Xu and X. Cui Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays Bioinformatics, April 15, 2008; 24(8): 1056 - 1062. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Koltai and C. Weingarten-Baror Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction Nucleic Acids Res., April 1, 2008; 36(7): 2395 - 2405. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. E. Bachmeier, I. V. Mohrenz, V. Mirisola, E. Schleicher, F. Romeo, C. Hohneke, M. Jochum, A. G. Nerlich, and U. Pfeffer Curcumin downregulates the inflammatory cytokines CXCL1 and -2 in breast cancer cells via NF{kappa}B Carcinogenesis, April 1, 2008; 29(4): 779 - 789. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Silkworth, E. A. Carlson, C. McCulloch, K. Illouz, S. Goodwin, and T. R. Sutter Toxicogenomic Analysis of Gender, Chemical, and Dose Effects in Livers of TCDD- or Aroclor 1254-Exposed Rats Using a Multifactor Linear Model Toxicol. Sci., April 1, 2008; 102(2): 291 - 309. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. F. Alcorn, A. S. Guala, J. van der Velden, B. McElhinney, C. G. Irvin, R. J. Davis, and Y. M. W. Janssen-Heininger Jun N-terminal kinase 1 regulates epithelial-to-mesenchymal transition induced by TGF-{beta}1 J. Cell Sci., April 1, 2008; 121(7): 1036 - 1045. [Abstract] [Full Text] [PDF]
|
|