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 variancemean 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:
![]() |
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] |
||||
![]() |
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] |
||||
![]() |
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] |
||||
![]() |
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., June 26, 2009; (2009) erp194v1. [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., June 15, 2009; (2009) gkp508v1. [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] |
||||
![]() |
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] |
||||
![]() |
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 1, 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 1, 2009; 38(1): 16 - 28. [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] |
||||
![]() |
A. M. McCord, M. Jamal, U. T. Shankavarum, F. F. Lang, K. Camphausen, and P. J. Tofilon Physiologic Oxygen Concentration Enhances the Stem-Like Properties of CD133+ Human Glioblastoma Cells In vitro Mol. Cancer Res., April 1, 2009; 7(4): 489 - 497. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. D. Silver, M. E. Ritchie, and G. K. Smyth Microarray background correction: maximum likelihood estimation for the normal-exponential convolution Biostat., April 1, 2009; 10(2): 352 - 363. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. A. Christianson, I. W. Wilson, D. J. Llewellyn, and E. S. Dennis The Low-Oxygen-Induced NAC Domain Transcription Factor ANAC102 Affects Viability of Arabidopsis Seeds following Low-Oxygen Treatment Plant Physiology, April 1, 2009; 149(4): 1724 - 1738. [Abstract] [Full Text] [PDF] |
||||
![]() |
B. Chetaille, F. Bertucci, P. Finetti, B. Esterni, A. Stamatoullas, J. M. Picquenot, M. C. Copin, F. Morschhauser, O. Casasnovas, T. Petrella, et al. Molecular profiling of classical Hodgkin lymphoma tissues uncovers variations in the tumor microenvironment and correlations with EBV infection and outcome Blood, March 19, 2009; 113(12): 2765 - 3775. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. J. Kim, R. Romero, C. J. Kim, A. L. Tarca, S. Chhauy, C. LaJeunesse, D.-C. Lee, S. Draghici, F. Gotsch, J. P. Kusanovic, et al. Villitis of Unknown Etiology Is Associated with a Distinct Pattern of Chemokine Up-Regulation in the Feto-Maternal and Placental Compartments: Implications for Conjoint Maternal Allograft Rejection and Maternal Anti-Fetal Graft-versus-Host Disease J. Immunol., March 15, 2009; 182(6): 3919 - 3927. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Xie, X. Wang, and M. Story Statistical methods of background correction for Illumina BeadArray data Bioinformatics, March 15, 2009; 25(6): 751 - 757. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. H. Talasaz, A. A. Powell, D. E. Huber, J. G. Berbee, K.-H. Roh, W. Yu, W. Xiao, M. M. Davis, R. F. Pease, M. N. Mindrinos, et al. Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device PNAS, March 10, 2009; 106(10): 3970 - 3975. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Azzouz, O. O. Panasenko, C. Deluen, J. Hsieh, G. Theiler, and M. A. Collart Specific roles for the Ccr4-Not complex subunits in expression of the genome RNA, March 1, 2009; 15(3): 377 - 383. [Abstract] [Full Text] [PDF] |
||||
![]() |
W. Qin, V. Haroutunian, P. Katsel, C. P. Cardozo, L. Ho, J. D. Buxbaum, and G. M. Pasinetti PGC-1{alpha} Expression Decreases in the Alzheimer Disease Brain as a Function of Dementia Arch Neurol, March 1, 2009; 66(3): 352 - 361. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Jans, J. M. Gladden, E. J. Ralston, C. S. Pickle, A. H. Michel, R. R. Pferdehirt, M. B. Eisen, and B. J. Meyer A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome Genes & Dev., March 1, 2009; 23(5): 602 - 618. [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] |
||||
![]() |
S. Bhattacharya, S. Srisuma, D. L. DeMeo, S. D. Shapiro, R. Bueno, E. K. Silverman, J. J. Reilly, and T. J. Mariani Molecular Biomarkers for Quantitative and Discrete COPD Phenotypes Am. J. Respir. Cell Mol. Biol., March 1, 2009; 40(3): 359 - 367. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. L. Bogan, M. J. Murphy, and J. D. Hennebold Dynamic Changes in Gene Expression that Occur during the Period of Spontaneous Functional Regression in the Rhesus Macaque Corpus Luteum Endocrinology, March 1, 2009; 150(3): 1521 - 1529. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Jergil, K. Kultima, A.-L. Gustafson, L. Dencker, and M. Stigson Valproic Acid-Induced Deregulation In Vitro of Genes Associated In Vivo with Neural Tube Defects Toxicol. Sci., March 1, 2009; 108(1): 132 - 148. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Nakamichi, M. Kusano, A. Fukushima, M. Kita, S. Ito, T. Yamashino, K. Saito, H. Sakakibara, and T. Mizuno Transcript Profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR Arrhythmic Triple Mutant Reveals a Role for the Circadian Clock in Cold Stress Response Plant Cell Physiol., March 1, 2009; 50(3): 447 - 462. [Abstract] [Full Text] [PDF] |
||||
![]() |
O. De la Cruz, R. Blekhman, X. Zhang, D. Nicolae, S. Firestein, and Y. Gilad A Signature of Evolutionary Constraint on a Subset of Ectopically Expressed Olfactory Receptor Genes Mol. Biol. Evol., March 1, 2009; 26(3): 491 - 494. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. S. Ojalvo, W. King, D. Cox, and J. W. Pollard High-Density Gene Expression Analysis of Tumor-Associated Macrophages from Mouse Mammary Tumors Am. J. Pathol., March 1, 2009; 174(3): 1048 - 1064. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Herve, P. Dabos, C. Bardet, A. Jauneau, M. C. Auriac, A. Ramboer, F. Lacout, and D. Tremousaygue In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development Plant Physiology, March 1, 2009; 149(3): 1462 - 1477. [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] |
||||
![]() |
S. C. Bangs, D. Baban, H. J. Cattan, C. K.-F. Li, A. J. McMichael, and X.-N. Xu Human CD4+ Memory T Cells Are Preferential Targets for Bystander Activation and Apoptosis J. Immunol., February 15, 2009; 182(4): 1962 - 1971. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Charafe-Jauffret, C. Ginestier, F. Iovino, J. Wicinski, N. Cervera, P. Finetti, M.-H. Hur, M. E. Diebel, F. Monville, J. Dutcher, et al. Breast Cancer Cell Lines Contain Functional Cancer Stem Cells with Metastatic Capacity and a Distinct Molecular Signature Cancer Res., February 15, 2009; 69(4): 1302 - 1313. [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. Tahvanainen, T. Kallonen, H. Lahteenmaki, K. M. Heiskanen, J. Westermarck, K. V. S. Rao, and R. Lahesmaa PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation Blood, February 5, 2009; 113(6): 1268 - 1277. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Baselga, M. Zambetti, A. Llombart-Cussac, G. Manikhas, E. Kubista, G. G. Steger, A. Makhson, S. Tjulandin, H. Ludwig, M. Verrill, et al. Phase II Genomics Study of Ixabepilone as Neoadjuvant Treatment for Breast Cancer J. Clin. Oncol., February 1, 2009; 27(4): 526 - 534. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Kenigsberg, Y. Bentov, V. Chalifa-Caspi, G. Potashnik, R. Ofir, and O. S. Birk Gene expression microarray profiles of cumulus cells in lean and overweight-obese polycystic ovary syndrome patients Mol. Hum. Reprod., February 1, 2009; 15(2): 89 - 103. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Zhang, J. Rowe, M. Kusel, A. Bosco, K. McKenna, N. de Klerk, P. D. Sly, and P. G. Holt Interleukin-10/Interleukin-5 Responses at Birth Predict Risk for Respiratory Infections in Children with Atopic Family History Am. J. Respir. Crit. Care Med., February 1, 2009; 179(3): 205 - 211. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Broet, S. Camilleri-Broet, S. Zhang, M. Alifano, D. Bangarusamy, M. Battistella, Y. Wu, M. Tuefferd, J.-F. Regnard, E. Lim, et al. Prediction of Clinical Outcome in Multiple Lung Cancer Cohorts by Integrative Genomics: Implications for Chemotherapy Selection Cancer Res., February 1, 2009; 69(3): 1055 - 1062. [Abstract] [Full Text] [PDF] |
||||
![]() |
H.-J. Kim, E. McMillan, F. Han, and C. N. Svendsen Regionally Specified Human Neural Progenitor Cells Derived from the Mesencephalon and Forebrain Undergo Increased Neurogenesis Following Overexpression of ASCL1 Stem Cells, February 1, 2009; 27(2): 390 - 398. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Sugio, R. Dreos, F. Aparicio, and A. J. Maule The Cytosolic Protein Response as a Subcomponent of the Wider Heat Shock Response in Arabidopsis PLANT CELL, February 1, 2009; 21(2): 642 - 654. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Oh, H. Kang, S. Yamaguchi, J. Park, D. Lee, Y. Kamiya, and G. Choi Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis PLANT CELL, February 1, 2009; 21(2): 403 - 419. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Delbes, D. Chan, P. Pakarinen, J. M. Trasler, B. F. Hales, and B. Robaire Impact of the Chemotherapy Cocktail Used to Treat Testicular Cancer on the Gene Expression Profile of Germ Cells from Male Brown-Norway Rats Biol Reprod, February 1, 2009; 80(2): 320 - 327. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. D. Meng, C. C. Shelton, Y.-M. Li, L.-X. Qin, D. Notterman, P. B. Paty, and G. K. Schwartz {gamma}-Secretase Inhibitors Abrogate Oxaliplatin-Induced Activation of the Notch-1 Signaling Pathway in Colon Cancer Cells Resulting in Enhanced Chemosensitivity Cancer Res., January 15, 2009; 69(2): 573 - 582. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. D. Raffel, G. C. Chu, J. L. Jesneck, D. E. Cullen, R. T. Bronson, O. A. Bernard, and D. G. Gilliland Ott1 (Rbm15) Is Essential for Placental Vascular Branching Morphogenesis and Embryonic Development of the Heart and Spleen Mol. Cell. Biol., January 15, 2009; 29(2): 333 - 341. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Huang, A. Greer, W. Hurlburt, X. Han, R. Hafezi, G. M. Wittenberg, K. Reeves, J. Chen, D. Robinson, A. Li, et al. The Mechanisms of Differential Sensitivity to an Insulin-like Growth Factor-1 Receptor Inhibitor (BMS-536924) and Rationale for Combining with EGFR/HER2 Inhibitors Cancer Res., January 1, 2009; 69(1): 161 - 170. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. L. Tarca, S. Draghici, P. Khatri, S. S. Hassan, P. Mittal, J.-s. Kim, C. J. Kim, J. P. Kusanovic, and R. Romero A novel signaling pathway impact analysis Bioinformatics, January 1, 2009; 25(1): 75 - 82. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Shen, N. Powers, N. Saini, C. E.S. Comstock, A. Sharma, K. Weaver, M. P. Revelo, W. Gerald, E. Williams, W. J. Jessen, et al. The SWI/SNF ATPase Brm Is a Gatekeeper of Proliferative Control in Prostate Cancer Cancer Res., December 15, 2008; 68(24): 10154 - 10162. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Kapur, H. Jiang, Y. Xing, and W. H. Wong Cross-hybridization modeling on Affymetrix exon arrays Bioinformatics, December 15, 2008; 24(24): 2887 - 2893. [Abstract] [Full Text] [PDF] |
||||
![]() |
B. A. Whitson, J. D'Cunha, R. S. Andrade, R. F. Kelly, S. S. Groth, B. Wu, J. S. Miller, R. A. Kratzke, and M. A. Maddaus Thoracoscopic Versus Thoracotomy Approaches to Lobectomy: Differential Impairment of Cellular Immunity Ann. Thorac. Surg., December 1, 2008; 86(6): 1735 - 1744. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Manos, J. Arthur, B. Rose, P. Tingpej, C. Fung, M. Curtis, J. S. Webb, H. Hu, S. Kjelleberg, M. D. Gorrell, et al. Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung J. Med. Microbiol., December 1, 2008; 57(12): 1454 - 1465. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. M. Kang, C. Ye, and E. Eskin Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots Genetics, December 1, 2008; 180(4): 1909 - 1925. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Malitsky, E. Blum, H. Less, I. Venger, M. Elbaz, S. Morin, Y. Eshed, and A. Aharoni The Transcript and Metabolite Networks Affected by the Two Clades of Arabidopsis Glucosinolate Biosynthesis Regulators Plant Physiology, December 1, 2008; 148(4): 2021 - 2049. [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] |
||||
![]() |
Y.-C. L. Tung, M. Ma, S. Piper, A. Coll, S. O'Rahilly, and G. S. H. Yeo Novel Leptin-Regulated Genes Revealed by Transcriptional Profiling of the Hypothalamic Paraventricular Nucleus J. Neurosci., November 19, 2008; 28(47): 12419 - 12426. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Hommais, C. Oger-Desfeux, F. Van Gijsegem, S. Castang, S. Ligori, D. Expert, W. Nasser, and S. Reverchon PecS Is a Global Regulator of the Symptomatic Phase in the Phytopathogenic Bacterium Erwinia chrysanthemi 3937 J. Bacteriol., November 15, 2008; 190(22): 7508 - 7522. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. E. Drew, K. J. Rodnick, M. Settles, J. Wacyk, E. Churchill, M. S. Powell, R. W. Hardy, G. K. Murdoch, R. A. Hill, and B. D. Robison Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio) Physiol Genomics, November 12, 2008; 35(3): 283 - 295. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. M. Mikheev, T. Nabekura, A. Kaddoumi, T. K. Bammler, R. Govindarajan, M. F. Hebert, and J. D. Unadkat Profiling Gene Expression in Human Placentae of Different Gestational Ages: An OPRU* Network and UW SCOR Study Reproductive Sciences, November 1, 2008; 15(9): 866 - 877. [Abstract] [PDF] |
||||
![]() |
L Lundholm, G Bryzgalova, H Gao, N Portwood, S Falt, K D Berndt, A Dicker, D Galuska, J R Zierath, J-A Gustafsson, et al. The estrogen receptor {alpha}-selective agonist propyl pyrazole triol improves glucose tolerance in ob/ob mice; potential molecular mechanisms J. Endocrinol., November 1, 2008; 199(2): 275 - 286. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. S. Chan and J. S. Song CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor Cancer Res., November 1, 2008; 68(21): 9041 - 9049. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. N. Simms and H. L. T. Mobley PapX, a P Fimbrial Operon-Encoded Inhibitor of Motility in Uropathogenic Escherichia coli Infect. Immun., November 1, 2008; 76(11): 4833 - 4841. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Xi, A. Feber, V. Gupta, M. Wu, A. D. Bergemann, R. J. Landreneau, V. R. Litle, A. Pennathur, J. D. Luketich, and T. E. Godfrey Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer Nucleic Acids Res., November 1, 2008; 36(20): 6535 - 6547. [Abstract] [Full Text] [PDF] |
||||















































