Application of machine learning and visualization of heterogeneous datasets to uncover relationships between translation and developmental stage expression of C. elegans mRNAs

Physiological Genomics

Volumn 21, Issue , 2005, Pages 264-273

  Trutschl, Marjan ^a,b   Dinkova, Tzvetanka D ^b   Rhoads, Robert E ^b  

^a Louisiana State University   (United States)

^b LOUISIANA STATE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

Author keywords

Caenorhabditis elegans; Color scale; eIF4E; mRNA specific translational control; Self organizing map

Indexed keywords

HELMINTH RNA; INITIATION FACTOR 4E;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOINFORMATICS; CAENORHABDITIS ELEGANS; DEVELOPMENTAL STAGE; DNA MICROARRAY; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LEARNING; NONHUMAN; PARASITE DEVELOPMENT; POLYSOME; PRIORITY JOURNAL; RNA TRANSLATION; TRANSLATION REGULATION;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; CAENORHABDITIS ELEGANS; EUKARYOTIC INITIATION FACTOR-4E; GENE EXPRESSION PROFILING; LINKAGE (GENETICS); MODELS, BIOLOGICAL; MODELS, THEORETICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYRIBOSOMES; PROTEIN BIOSYNTHESIS; PROTEIN ISOFORMS; RNA, MESSENGER;

CAENORHABDITIS ELEGANS;

EID: 21244473003     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00307.2004     Document Type: Article

References (19)

1. Chalfie M, Tu Y, Euskirchen G, Ward WW, and Prasher DC. Green fluorescent protein as a marker for gene expression. Science 263: 802-805, 1994.
2. Dinkova TD, Keiper BD, Korneeva NL, Aamodt EJ, and Rhoads RE. Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform. Mol Cell Biol 25: 100-113, 2005.
3. Eisen MB, Spellman PT, Brown PO, and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868, 1998.
4. Gasch AP and Eisen MB. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3: 59.51-59.22, 2002.
5. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, and Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286: 531-537, 1999.
6. Jankowska-Anyszka M, Lamphear BJ, Aamodt EJ, Harrington T, Darzynkiewicz E, Stolarski R, and Rhoads RE. Multiple isoforms of eukaryotic protein synthesis initiation factor 4E in C. elegans can distinguish between mono- and trimethylated mRNA cap structures. J Biol Chem 273: 10538-10542, 1998.
7. Jiang M, Ryu J, Kirlay M, Duke K, Reinke V, and Kim SK. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc Natl Acad Sci USA 98: 218-223, 2001.
8. Keiper BD, Lamphear BJ, Deshpande AM, Jankowska-Anyszka M, Aamodt EJ, Blumenthal T, and Rhoads RE. Functional characterization of five eIF4E isoforms in Caenorhabditis elegans. J Biol Chem 275: 10590-10596, 2000.
9. Kohonen T. Self-Organizing Maps. Berlin: Springer-Verlag, 1995.
10. Levkowitz H. Color Theory and Modeling for Computer Graphics, Visualization, and Multimedia Applications. Boston, MA: Kluwer Academic, 1997.
11. Lodish HF. Model for the regulation of mRNA translation applied to haemoglobin synthesis. Nature 251: 385-388, 1974.
12. Roy PJ, Stuart JM, Lund J, and Kim SK. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418: 975-979, 2002.
13. Sonenberg N, Hershey JWB, and Mathews MB. Translational Control of Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 2000.
14. Stachelska A, Wieczorek Z, Ruszczynska K, Stolarski R, Pietrzak M, Lamphear BJ, Rhoads RE, Darzynkiewicz E, and Jankowska-Anyszka M. Interaction of three Caenorhabditis elegans isoforms of translation initiation factor eIF4E with mono- and trimethylated mRNA 5′ cap analogues. Acta Biochim Pol 49: 671-682, 2002.
15. Sulston J and Horovitz HR. Post-embryonic cell lineages of the nematode Caenorhabditis elegans. Dev Biol 56: 110-156, 1977.
16. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, and Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912, 1999.
17. Wang J and Kim SK. Global analysis of dauer gene expression in Caenorhabditis elegans. Development 130: 1621-1634, 2003.
18. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A, Bussemaker HJ, Kim SK, and Chalfie M. Identification of genes expressed in C elegans touch receptor neurons. Nature 418: 331-335, 2002.
19. Zong Q, Schummer M, Hood L, and Morris DR. Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc Natl Acad Sci USA 96: 10632-10636, 1999.