Transporter and ion channel gene expression after caco-2 cell differentiation using 2 different microarray technologies

Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome.Science. 2001;291:1304–1351. Hughes TR, Marton MJ, Jones AR, et al. Functional discovery via a compendium of expression profiles.Cell. 2000;102:109–126. Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays.Nature. 2000;405:827–836. Sun D, Lennernas H, Welage LS, et al. Comparison of human duodenum and Caco-2 gene expression profiles for 12,000 gene sequences tags and correlation with permeability of 26 drugs.Pharm Res. 2002;19:1400–1416. Chay CH, Cooper CR, Gendernalik JD, et al. A functional thrombin receptor (PAR1) is expressed on bone-derived prostate cancer cell lines.Wrology. 2002;60:760–765. Landowski CP, Sun D, Foster DR, et al. Gene expression in the human intestine and correlation with oral valacyclovir pharmacokinetic parameters.J Pharmacol Exp Ther. 2003;306:778–786. Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays.Nat Biotechnol. 1996;14:1675–1680. Anderle P, Rakhmanova V, Woodford K, Zerangue Z, Sadee W. Messenger RNA expression of transporter and ion channel genes in undifferentiated and differentiated Caco-2 cells compared to human intestine.Pharm Res. 2003;20:3–15. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays.Nucleic Acids Res. 2000;28:4552–4557. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science. 1995;270:467–470. Anderle P, Duval M, Draghici S, Kuklin A, Littlejohn TG, Medrano JF, Vilanova D, Roberts MA. Gene expression databases and data mining.Biotechniques. 2003;Mar(suppl):36–44. Ishii M, Hashimoto S, Tsutsumi S, et al. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis.Genomics. 2000;68:136–143. Bittner M. Obtaining and evaluating gene expression profiles with cDNA microarrays. In: Suhai S, ed.Genomics and Proteomics. New York, NY: Kluwer, 2000:5–25. Li J, Pankratz M, Johnson JA. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays.Toxicol Sci. 2002;69:383–390. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS. Analysis of matched mRNA measurements from 2 different microarray technologies.Bioinformatics. 2002;18:405–412. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC. Accuracy and calibration of commercial oligonucleotide and custom cDNA arrays.Nucleic Acids Res. 2002;30:e48. Tan PK, Downey TJ, Spitznagel EL, et al. Evaluation of gene expresion measurements from commercial microarray platforms.Nucleic Acids Res. 2003;31:5676–5684. Barezak A, Rodriguez MW, Hanspers K, et al. Spotted long oligonucleotide arrays for human gene expression analysis.Genome Res. 2003;13:1775–1785. Yang MC, Ruan QG, Yang JJ, et al. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays.Physiol Genomics. 2001;7:45–53. Shin HC, Landowski CP, Amidon GL. Transporters in the GI tract. In: Waterbeemd V-d, Lennernäs H, Artursson P, eds.Drug Bioavailability/Estimation of Solubility, Permeability and Absorption. Weinheim Germany: Wiley-VCH; 2003. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale.Science. 1997;278:680–686. Yang YH, Dudoit S, Luu P, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple systematic variation.Nucleic Acids Res. 2002;30:e15. Mariadason JM, Corner GA, Augenlicht LH. Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin a, sulindac, and curcumin and implications for chemoprevention of colon cancer.Cancer Res. 2000;60:4561–4572. Mariadason JM, Arango D, Corner GA, e al. A gene expression profile that defines colon cell maturationin vitro.Cancer Res. 2002;62:4791–4804. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Within the fold: assessing differential expression measures and reproducibility in microarray assays.Genome Biol. 2002, 3(11): research0062.1-0062.12. Pedron T, Thibault C, Sansonetti PJ. The invasive phenotype ofShigella flexneri directs a distinct gene expression pattern in the human intestinal epithelial cell line Caco-2.J Biol Chem. 2003;278:33878–33886. Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls.Genome Biol. 2001;2(12):research0055. Zarrinkar PP, Mainquist JK, Zamora M, et al. Arrays of arrays for highthroughput gene expression profiling.Genome Res. 2001;11:1256–1261. Baum M, Bielau S, Rittner N, et al. Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling.Nucleic Acids Res. 2003;31:e151. Engle MJ, Goetz GS, Alpers DH. Caco-2 cells express a combination of colonocyte and enterocyte phenotypes.J Cell Physiol. 1998;174:362–369. Levy P, Robert A, Picard J. Biosynthesis of glycosaminoglycans in the human colonic tumor cell line Caco-2: structural changes occurring with the morphological differentiation of the cells.Biol Cell. 1988;62:255–264. Hidalgo IJ, Raub TJ, Borchardt RT. Characterization of the human colon carcinoma cell line (Caco-2) as a model system for intestinal epithelial permeability.Gastroenterology. 1989;96:736–749. Rothen-Rutishauser B, Braun A, Günthert M, Wunderli-Allenspach H. Formation of multilayers in the Caco-2 cell culture model: a confocal laser scanning microscopy study.Pharm Res. 2000;17:460–465. Mariadason JM, Kurt L, Rickard KL, David H, Barkla DH, Augenlicht LH, Gibson PR. Divergent phenotypic patterns and commitment to apoptosis of Caco-2 cells during spontaneous and butyrateinduced differentiation.J Cell Physiol. 2000;183:347–354. Fleet JC, Wang L, Vitek O, Craig BA, Edenberg HJ. Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation.Physiol Genomics. 2003;13:57–68. Behrens I, Kissel T. Do cell culture conditions influence the carriermediated transport of peptides in Caco-2 cell monolayers?Eur J Pharm Sci. 2003;19:433–442. Bravo SA, Nielsen CU, Amstrup J, Frokjaer S, Brodin B. In-depth evaluation of Gly-Sar transport parameters as a function of culture time in the Caco-2 cell model.Eur J Pharm Sci. 2004;21:77–86. Kothapalli R, Yoder SJ, Mane S, Loughran TP Jr. Microarray results: how accurate are they?BMC Bioinformatics. 2002;3:22. Geller SC, Gregg JP, Hagerman P, Rocke DM. Transformation and normalization of oligonucleotide microarray data.Bioinformatics. 2003;19:1817–1823. Tseng GC, Oh M-K, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.Nucleic Acids Res. 2001;15:2549–2557.