Bioinformatics F & S Core

      Welcome to University of Cincinnati's

Center for Environmental Genetics

Microarray Analysis Homepage

We are providers of comprehensive microarray analysis support and bioinformatics services.  

Our services include:

• Analysis of two-channel, Affymetrix, or Codelink platforms

• expression arrays, tiling (promoter) arrays, miRNA, CGH arrays

• helping investigators determine the optimal experimental design, 

• non-linear data normalization, multi-way ANOVA (MIXED model) analysis, and Bayesian moderated-T adjustment

• various visualizations of data, 

• clustering analyses (all commonly used methods, plus Mario Medvedovic's bayesian infinite mixture method, see ref below)

• the incorporation of annotations, gene ontology (GO) information, or other functional group analyses

• custom-tailored analyses for individual questions

• comparison of multiple experiments, including between platforms, array types, and different species. 

• separate analysis for genes involved in biological functions of interest.  

• Write up of statistical procedures used for publication

   Because our analysis methods are flexible, we are able to incorporate the latest techniques and stay up-to-date with all the latest microarray analysis research. 

Tips for Optimizing your Experimental Design

Microarray Myths and Truths

Determining number of replicates needed to detect differentially expressed genes

Fundamentals of experimental design for cDNA microarrays from Nature Genetics

(be sure to read the box insert entitled "Allocating resources in a microarray experiment")

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Who are we?

Mario Medvedovic, PhD                      Maureen Sartor, MBMA

                                          

Res. Assistant Professor                            Bioinformatics Res. Associate

Mario.Medvedovic@uc.edu                      Sartorma@ucmail.uc.edu

(513)558-8564                                         (513)558-6781

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Microarray-related Publications   Sartor MA, Tomlinson CR, Wesselkamper SC, Sivaganesan S, Leikauf GD, and Medvedovic M. Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. BMC Bioinformatics 7(1): 538, 2006. (Support Page) Sartor MA, Zorn AM, Schwanekamp JA, Halbleib D, Karyala S, Howell ML, Dean GE,  Medvedovic M, Tomlinson CR. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nuc Acids Res. 2006; 34(1):185-200. Schwanekamp JA, Sartor MA, Karyala S, Halbleib D, Medvedovic M, Tomlinson CR. Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin. Biochim Biophys Acta. 1759(8-9): 388-402, 2006. Mesa C, Mirza M, Mitsutake N, Sartor M, Medvedovic M, Tomlinson C, Knauf JA, Weber GF, Fagin JA. Conditional activation of RET/PTC3 and BRAFV600E in thyroid cells is associated with gene expression profiles that predict a preferential role of BRAF in extracellular matrix remodeling. Cancer Res. 2006; 66(13): 6512-9. Deng M, Chen WL, Takatori A, Peng Z, Zhang L, Mongan M, Parthasarathy R, Sartor M, Miller M, Yang J, Su B, Kao WW, Xia Y. A role for the mitogen-activated protein kinase kinase kinase 1 in epithelial wound healing. Mol Biol Cell. 2006; 17(8): 3446-55. Erwin CR, Jarboe MD, Sartor MA, Medvedovic M, Stringer KF, Warner BW, Bates MD. Developmental characteristics of adapting mouse small intestine crypt cells. Gastroenterology. 2006; 130(4):1324-32. Wesselkamper S.C., Case L.M., Henning L.M., Borchers M.J., Tichelaar J.W., Medvedovic M., Sartor M.A., Tomlinson C.R., Leikauf G.D..  Gene expression changes during acute lung injury: role of transforming growth factor-beta. Am J Respir Crit Care Med., Aug 2005; Epub. Wesselkamper S.C., McDowell S.A., Medvedovic M., Dalton T.P., Deshmukh H.S., Sartor M.A., Case L.M., Henning L.M., Borchers M.J., Tomlinson C.R., Prows D.R., Leikauf G.D.. The role of metallothionein in the pathogenesis of acute lung injury. Am J Respir Cell Mol Biol. Sep 2005; Epub. Puxeddu E., Knauf J.A., Sartor M.A., Mitsutake N., Smith E.P., Medvedovic M., Tomlinson C.R., Moretti S., Fagin J.A. RET/PTC-induced gene expression in thyroid PCCL3 cells reveals early activation of genes involved in regulation of the immune response. Endocr Relat Cancer. 12(2):319-34, 2005. Sartor M., Schwanekamp J., Halbleib D., Mohamed I., Karyala S., Medvedovic M., Tomlinson C.R..  Microarrays are significantly improved as hybridization approaches equilibrium. Biotechniques. 36(5):790-6, May 2004. Bahassi,el M., Karyala,S., Tomlinson,C.R., Sartor,M.A., Medvedovic,M., Hennigan,R.F.: Critical regulation of genes for tumor cell migration by AP-1. Clin. Exp. Metastasis. 21(4):293-304, 2004 Kann S., Huang M., Estes C., Reichard J.F., Sartor M.A., Xia Y., Puga A.: Arsenite-induced aryl hydrocarbon receptor nuclear translocation results in additive induction of phase I and synergistic induction of phase II genes. Mol. Pharm. 68:336-346, 2005.  Kann S., Estes C., Reichard R.F., Huang M.-Y., Sartor M.A., Schwemberger S., Chen Y., Dalton T.P., Shertzer H.G., Xia Y., Puga A. Butylhydroquinone protects cells genetically deficient in glutathione biosynthesis from arsenite-induced apoptosis without significantly changing their prooxidant status. Toxicol Sci 87:365-384, 2005.  Leikauf G.D., Wesselkamper SC, Bachurski C., Medvedovic M., Sartor M.A., Tomlinson C.R.,. McDowell S.A., Case L.M., Haffey B.D., Henning L.M.,Horner M.L., Hardie W.D., Korfhagen T.R, Prows D.R.: Transcriptional Regulatory Networks in Acute Lung Injury. In: Effects of Air Contaminants on the Respiratory Tract – Interpretations from Molecules to Meta Analysis. U. Heinrich (ed.), Fraunhofer IRB Verlag, Stuutgart, 373-96,2004. Leikauf G.D., Hardie W.D., Wesselkamper S.C., Bachurski C.J., Medvedovic M., Sartor M.A., Tomlinson C.R., McDowell S.A., Henning L.M., Case L.M., Tichelaar J.W., Prows D.R., Korfhagen T.R,: Resolving Gene-Environment Interactions in Complex Traits: Acute Lung Injury. Am J. Respir. Cell Mol Biol. (In press). Leikauf G.D., Haffey B.D., Horner M.L., Medvedovic M., Sartor M.A., Tomlinson C.R., Henning L.M., Case L.M.,Wesselkamper SC, Singer, J.B., Hill A., Lander E.S. Nadeau J.H., Prows D.R.: Assessment of a functional candidate gene for acute lung injury in mice: Thyroid hormone receptor-alpha.. Am J. Respir. Cell Mol Biol. (Submitted). Zhang J., Moseley A., Jegga A.G., Gupta A., Witte D.P., Sartor M., Medvedovic M., Williams S.S., Ley-Ebert C., Coolen L., Egnaczyk G., Genter M.B., Lehman M., Lingrel J., Maggio J., Parysek L., Walsh R., Xu M., Aronow B.J. Neural system-enriched gene expression, relationship to biological pathways and neurological diseases.  Physiol Genomics. 18(2):167-83, 2004. M. Sartor, M. Medvedovic, and B. Aronow. "Microarray data normalization: the art and science of overcoming technical variance to maximize the detection of biologic variance."  A Beginner's Guide to Microarrays. Ch. 5:151-178, ed. Eric Blalock, Kluwer Academic Publishers, 2003. Medvedovic, M., Yeung, K.Y., Bumgarner, R.E. Bayesian mixture model based clustering of replicated microarray data. Bioinformatics. 20(8):1222-32, 2004. A. Puga, M. Sartor, M. Huang, J.K. Kerzee, Y. Wei, C. Tomlinson, C.S. Baxter and M. Medvedovic. Gene expression profiles of mouse aorta and cultured vascular smooth muscle cells are widely different, yet show common responses to dioxin exposure.  Cardiovascular Toxicology. 4(4): 385-403, 2004. Y. Wei, K. Tepperman, M. Huang, M. Sartor and A. Puga. Chromium inhibits transcription from PAH-inducible promoters by blocking the release of HDAC and preventing the binding of p300 to chromatin. J. of Biol Chem.  2004; 279(6):4110-9.  Karyala, S., J. Guo, M. Sartor, M. Medvedovic, S. Kann, A. Puga, P. Ryan, and C.R. Tomlinson. (2004). Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice. Cardiovasc. Toxicol. 4(1):47-74, 2004. Junhai Guo, Maureen Sartor, Saikumar Karyala, Mario Medvedovic, Simone Kann, Alvaro Puga, Patrick Ryan, and Craig R. Tomlinson. Expression of genes in the TGF-β signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice.  Toxicology and Applied Pharmacology. 2004; 194(1):79-89.      Morgan KT, Ni H, Brown HR, Yoon L, Qualls CW, Crosby LM, Reynolds R, Gaskill B, Anderson SP, Kepler TB, Brainard T, Liv N, Easton M, Merrill C, Creech D, Sprenger D, Conner G, Johnson Pr, Fox T, Sartor M, Richard E, Kuruvilla S, Casey W, Benavides G. Application of cDNA microarray technology to in vitro toxicology and the selection of genes for a RT-PCR-based screen for oxidative stress in Hep-G2 cells.  Toxicol Pathol. 2002 Jul-Aug; 30(4):435-51. Hester SD, Benavides GB, Sartor M, Yoon L, Wolf DC, Morgan KT.  Normal gene expression in male F344 rat nasal transitional and respiratory epithelium.  Gene. 2002 Feb 20; 285(1-2):301-10. Medvedovic M, Sivaganesan S.  Bayesian infinite mixture model based clustering of gene expression profiles.  Bioinformatics. 2002 Sep;18(9):1194-206. Puga A, Maier A, Medvedovic M.  The transcriptional signature of dioxin in human hepatoma HepG2 cells.  Biochem Pharmacol. 2000 Oct 15;60(8):1129-42. Yeung KY, Medvedovic M, Bumgarner R.  Clustering gene-expression data with repeated measurements.  Genome Biology. 2003 April; 4(5): R34.

UC Links and Contact Info   UC Genomics and Microarray Laboratory's (GML) website:  http://microarray.uc.edu/,  Rm. 336 Kettering Laboratory (513)558-4764   Mario Medvedovic's Computational Systems Biology Lab   UC's Mass Spectrometry Facility   UC's Proteomics Core Center for Environmental Genetics (CEG) Bruce Aronow's Homepage Bioinformatics Workshop Summary- Microarray Analysis, November 12th, 2002

-This page was  SC updated on 01/22/2007 by Maureen Sartor.

Department of Environmental Health University of Cincinnati
PO Box 670056 Cincinnati, OH 45267-0056   

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