References to related exploratory data analysis methods and MAExplorer

This short list of references is limited to a few related to exploratory data analysis methods for microarrays as they relate to MAExplorer. It is not meant to be inclusive. More extensive lists of references to many of the array preparation and data mining methods can be found in some of these papers and on the Internet.

  1. Beardsly T (1999) Scientific American, March 1999, 35-36.

  2. Bickel, D (2001) "Robust Cluster Analysis of DNA Microarray Data: An Application of Nonparametric Correlation Dissimilarity. Proceedings of the Joint Statistical Meetings of the American Statistical Association (Biometrics Section, to appear). []

  3. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genetics 28: 365-371. [See, and]

  4. Cleveland WS (1985) The Elements of Graphing Data. Wadsworth Press, Monterey, CA, pp 1-323.

  5. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM (1996) Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nature Genetics 1996, 14: 457-460.

  6. Dudoit S, Yang YH, Callow MJ, Speed TP (2000,Aug) Statistical methods for identifying differentially expressed genes in replicated microarrays experiments. TR-578, Dept. of Statistics, Stanford Univ., Stanford, CA.

  7. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. PNAS USA 95: 14863-14868.

  8. Jagota, A (2001) Microarray Data Analysis and Visualization. Bioinformatics By The Bay Press, 101 pp. ISBN-09700297-3-X.

  9. Kaufman L, Rousseeuw PJ (1990) Finding Groups in Data: An Introduction to Cluster Analysis. J. Wiley and Sons, Inc., New York.

  10. Kerr MK, Churchill GA (2001) Statistical design and the analysis of gene expression microarray data. Genet Res. 77(2):123-8. Review.

  11. Kerr MK, Churchill GA (2001) Bootstraping cluster analysis: Assessing the reliability of conclusions from microarray experiments. PNAS 98:8961-8965.

  12. Korn EL, Troendle JF, McShane LM, Simon R (2001) Controlling the number of false discoveries: Application to high-dimensional genomic data. BRB, NCI, Bethesda, MD. Aug 22, 2001, Tech Report #3.

  13. Lipkin LE, Lemkin PF (1980) Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. Clin. Chem. 26: 1403-1412. (GELLAB-II home page

  14. Lemkin PF, Lester EP (1989) Database and search techniques for two-dimensional gel protein data: a comparison of paradigms for exploratory data analysis and prospects for biological modeling. Electrophoresis 10: 122-140.

  15. Lemkin PF (1995) Representations of protein patterns from 2D gel electrophoresis databases. In: Pickover, C., (Ed) The Visual Display of Biological Information, World Scientific Publishers, River Edge, New Jersey, pp 43-59.

  16. Lemkin PF (1993) Xconf: a network-based image conferencing system. Comput. Biomed. Res. 26, 1-27.

  17. Lemkin PF (1997) Comparing Two-Dimensional electrophoretic gels across the Internet. Electrophoresis, 18: 461-470. [Extended paper], (Web site

  18. Lemkin PF, Thornwall G (1999a) Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database. Molecular Biotechnology, 12:(2) 159-172. [Extended paper and Web site]

  19. Lemkin PF, Myrick JM, Lakshmanan Y, Shue MJ, Patrick JL, Hornbeck PV, Thornwall GC, Partin AW (1999b) Exploratory Data Analysis Groupware for Qualitative and Quantitative Electrophoretic Gel Analysis Over the Internet - WebGel. Electrophoresis 20:(18) 3492-507. (PDF), (also see WebGel server:

  20. Lemkin PF, Thornwall GC, Walton KD, Hennighausen L (2000) The Microarray Explorer tool for data mining of cDNA microarrays - application for the mammary gland Nucleic Acid Research 28:(22) 4452-4459. (PDF).

  21. Lemkin PF, Thornwall GC, Walton KD, Hennighausen L (2000) MicroArray Explorer - a tool for data mining of microarrays - Overview. (PDF).

  22. Lemkin PF, Thornwall GC, Walton KD, Hennighausen L (2000) MicroArray Explorer - a tool for data mining of microarrays - Examples. (PDF).

  23. Lemkin PF, Thornwall GC, Powell J, Asaki E (2000) Using MAExplorer with the NCI/CIT mAdb Web server. (PDF) and []

  24. Lemkin PF (2001) Introduction to Data Mining of Microarrays using the MicroArray Explorer. (PDF) or (PPT).

  25. Lemkin PF (2001) Using Cvt2Mae to convert Affymetrix array data for MAExplorer. (PDF)

  26. Lemkin PF, Thornwall G, Hennighausen L (2001) MicroArray Explorer - A Java-based Tool For Data Mining Microarrays. Paper presented at the AMS-IMS-SIAM Summer Conference on Statistics in Functional Genomics, June 10-14, 2001. (PDF).

  27. McShane LM, Radmacher MD, Freidlin B, Yu R, Li M-C, Simon R (2001) Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. BRB, NCI, Bethesda, MD. July 1, 2001, Tech Report #2.

  28. Radmacher MD, McShane LM, Simon R (2001) A paradigm for class prediction using gene expression profiles. BRB, NCI, Bethesda, Nov 19, 2001, Tech Report #1.

  29. Schneiderman B (1997) Designing the Human Interface, 3rd edition. Addison-Wesley Pub. Co., NY, pp 1-638.

  30. Schulze A, Downward J (2001) Navigating gene expression using microarrays - a technology review. Nature Cell Biology 3: E190-E195.

  31. Simon R, Radmacher MD, Dobbin K (2001) Design of Studies Using DNA Microarrays. BRB, NCI, Bethesda, MD. 2001, Tech Report #4.

  32. Sneath PHA, Sokol RR (1973) Numerical taxonomy. W.H. Freeman and Co, San Francisco. pp 1-573.

  33. StatSoft Inc. (2002) Electronic Statistics Textbook, Tulsa, OK: StatSoft. Available at

  34. Tufte E (1997) Visual Explanations. Images and quantities, evidence and narrative. Graphics Press, Cheshire, CT, pp 1-156.

  35. Tukey J (1977) Exploratory data analysis. Addison-Wesley Pub. Co., Reading, MA, pp 1-688.

  36. Vawter MP, Barrett T, Cheadle C, Sokolov BP, Wood WH III, Donovan DM, Webster M, Freed WJ, Becker KG (2000) Application of cDNA Microarrays to Examine Gene Expression Differences in Schizophrenia. Submitted.

  37. Weinstein JN, Myers TG, O'Conner PM, Friend SH, Fornace AJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johynson GS, Wittes RE, Paull KD(1997) An Inforation-Intensive Approach to the Molecular Pharmacology of Cancer. Science 275: 343-349.

  38. White KP, Rifkin SA, Hurban P, Hogness DS (1999) Microarray Analysis of Drosophila Development during Metamorphosis. Science 286: 2179-2184.