Artificial Intelligence in Medicine
Volume 35, Issue 1 , Pages 49-60 , September 2005

SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor

  • Daniel Dvorkin

      Affiliations

    • University of Colorado at Denver and Health Sciences Center, Denver, CO 80217, USA
    • University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
    • Corresponding Author InformationCorresponding author at: 1138 E. 14th Ave. Unit 8, Denver, CO 80218, USA. Tel.: +1 303 548 4568; fax: +1 303 607 9430.
    • ,
  • Valerie Fadok

      Affiliations

    • National Jewish Medical and Research Center, Denver, CO 80206, USA
    • ,
  • Krzysztof Cios

      Affiliations

    • University of Colorado at Denver and Health Sciences Center, Denver, CO 80217, USA
    • University of Colarado at Boulder, CO 80309, USA
    • 4C Data LLC, Golden, CO 80401, USA

Received 11 October 2004 ,Revised 9 January 2005 ,Accepted 12 January 2005.

References 

  1. McDonald P, Fadok V, Bratton D, Henson P. Transcriptional and translational regulation of inflammatory mediator production by endogenous TGF- in macrophages that have ingested apoptotic cells. J Immunol. 1999;163:6164–6172
  2. Vandivier R, Fadok V, Hoffman P, Bratton D, Penvari C, Brown K, et al. Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. J Clin Invest. 2002;109:661–670
  3. Henson P, Bratton D, Fadok V. The phosphatidylserine receptor: a crucial molecular switch. Nat Rev: Mol Cell Biol. 2001;2:627–633
  4. Jarvis RA, Patrick EA. Clustering using a similarity measure based on shared near neighbors.. IEEE Trans Comput. 1973;C22(11):1025–1034
  5. Cios K, Pedrycz W, Swiniarski R. Data mining methods for knowledge discovery. Norwell, MA: Kluwer Academic Publishers; 1998;
  6. Devore JL. Probability and statistics for scientists and engineers. Pacific Grove, CA: Duxbury; 2000;
  7. Friedberg SH, Insel AJ, Spence LE. Linear algebra. 3rd ed.. Upper Saddle River, NJ: Prentice Hall; 1997;
  8. Affymetrix Inc., Statistical algorithms description document, http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf (accessed: 17 January 2005), 2002.
  9. Gwinn MR, Whipkey DL, Weston A. The effect of oxythioquinox exposure on normal human mammary epithelial cell gene expression: a microarray analysis study. Environmental Health; 2004 (E-publication ahead of print).
  10. Hashimoto M, Koda M, Ino H, Yoshinaga K, Murata A, Yamazaki M, Kojima K, Chiba K, Mori C, Moriya H. Gene expression profiling of cathepsin D, metallothioneins-1 and -2, osteopontin, and tenascin-C in a mouse spinal cord injury model by cDNA microarray analysis. Acta Neuropathol; 2004 (E-publication ahead of print).
  11. Nguyen DH, Toshida H, Schurr D, Beuerman RW. Microarray analysis of the rat lacrimal gland following the loss of parasympathetic control of secretion. Physiol Genomics. 2004;18(1):108–118
  12. Kim H, Golub GH, Park H. Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics; 2004 (E-publication ahead of print).
  13. Taguchi YH, Oono Y, Relational patterns of gene expression via nonmetric multidimensional scaling analysis. Bioinformatics; 2004 (E-publication ahead of print).
  14. Zorn KK, Jazaeri AA, Awtrey CS, Gardner GJ, Mok SC, Boyd J, et al. Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies. Clin Cancer Res. 2003;9:4811–4818
  15. He X, Weyand CM, Goronzy JJ, Zhong W, Stuart JM. Bi-directional modulation of T cell-dependent antibody production by prostaglandin . Int Immunol. 2002;14(1):69–77
  16. deHoon M, Imoto S, Miyano S. The C Clustering Library, 2002, http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster/cluster.pdf (accessed: 17 January 2005).
  17. Pan W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics. 2002;18(4):546–554

PII: S0933-3657(05)00060-6

doi: 10.1016/j.artmed.2005.01.010

Artificial Intelligence in Medicine
Volume 35, Issue 1 , Pages 49-60 , September 2005

Article Tools

* Image Usage & Resolution