Dynamic expression profiles from static cytometry data: Component fitting and conversion to relative, "same scale" values

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Avva, Jayant ^a   Weis, Michael C ^a   Sramkoski, R Michael ^b   Sreenath, Sree N ^a   Jacobberger, James W ^b  

^a Case Western Reserve University   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; CYCLIN A2; CYCLIN B1; DNA; EPITOPE; HISTONE H3; PROPIDIUM IODIDE;

ARTICLE; CALCULATION; CELL CYCLE G1 PHASE; CELL CYCLE M PHASE; CELL CYCLE S PHASE; CELL STRAIN K 562; CONTROLLED STUDY; CYTOMETRY; FLOW CYTOMETRY; HUMAN; HUMAN CELL; IMMUNOFLUORESCENCE; INTERPHASE; MITOSIS; PROTEIN EXPRESSION;

CELL CYCLE; CYCLIN A2; CYCLIN B1; EPITOPES; FLOW CYTOMETRY; GENE EXPRESSION; HISTONES; HUMANS; IMMUNOHISTOCHEMISTRY; INDOLES; K562 CELLS; LINEAR MODELS; PROPIDIUM;

EID: 84863764186     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038275     Document Type: Article

References (33)

1. Csikasz-Nagy A, Battogtokh D, Chen KC, Novak B, Tyson JJ, (2006) Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J 90: 4361-4379.
2. Novak B, Tyson JJ, (2004) A model for restriction point control of the mammalian cell cycle. J Theor Biol 230: 563-579.
3. Jacobberger JW, Avva J, Sreenath SN, Weis MC, Stefan T, (2012) Dynamic epitope expression from static cytometry data: principles and reproducibility. PLoS One.
4. Bazile F, St-Pierre J, D'Amours D, (2010) Three-step model for condensin activation during mitotic chromosome condensation. Cell Cycle 9: 3243-3255.
5. Koseoglu MM, Dong J, Marzluff WF, (2010) Coordinate regulation of histone mRNA metabolism and DNA replication: cyclin A/cdk1 is involved in inactivation of histone mRNA metabolism and DNA replication at the end of S phase. Cell Cycle 9: 3857-3863.
6. Frisa PS, Lanford RE, Jacobberger JW, (2000) Molecular quantification of cell cycle-related gene expression at the protein level. Cytometry 39: 79-89.
7. Frisa PS, Jacobberger JW, (2009) Cell cycle-related cyclin b1 quantification. PLoS One 4: e7064.
8. Jacobberger JW, Sramkoski RM, Wormsley SB, Bolton WE, (1999) Estimation of kinetic cell-cycle-related gene expression in G1 and G2 phases from immunofluorescence flow cytometry data. Cytometry 35: 284-289.
9. Erlandsson F, Linnman C, Ekholm S, Bengtsson E, Zetterberg A, (2000) A detailed analysis of cyclin A accumulation at the G(1)/S border in normal and transformed cells. Exp Cell Res 259: 86-95.
10. Gong J, Traganos F, Darzynkiewicz Z, (1995) Growth imbalance and altered expression of cyclins B1, A, E, and D3 in MOLT-4 cells synchronized in the cell cycle by inhibitors of DNA replication. Cell Growth Differ 6: 1485-1493.
11. Singhania R, Sramkoski RM, Jacobberger JW, Tyson JJ, (2011) A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol 7: e1001077.
12. Crosio C, Fimia GM, Loury R, Kimura M, Okano Y, et al. (2002) Mitotic phosphorylation of histone H3: spatio-temporal regulation by mammalian Aurora kinases. Mol Cell Biol 22: 874-885.
13. Monier K, Mouradian S, Sullivan KF, (2007) DNA methylation promotes Aurora-B-driven phosphorylation of histone H3 in chromosomal subdomains. J Cell Sci 120: 101-114.
14. Scrittori L, Skoufias DA, Hans F, Gerson V, Sassone-Corsi P, et al. (2005) A small C-terminal sequence of Aurora B is responsible for localization and function. Mol Biol Cell 16: 292-305.
15. Jacobberger JW, Frisa PS, Sramkoski RM, Stefan T, Shults KE, et al. (2008) A new biomarker for mitotic cells. Cytometry A 73: 5-15.
16. Pines J, (2009) The APC/C: a smorgasbord for proteolysis. Mol Cell 34: 135-136.
17. Izawa D, Pines J, (2011) How APC/C-Cdc20 changes its substrate specificity in mitosis. Nat Cell Biol 13: 223-233.
18. Pines J, (2011) Cubism and the cell cycle: the many faces of the APC/C. Nat Rev Mol Cell Biol 12: 427-438.
19. Viallard JF, Lacombe F, Dupouy M, Ferry H, Belloc F, et al. (1999) Flow cytometry study of human cyclin B1 and cyclin E expression in leukemic cell lines: cell cycle kinetics and cell localization. Exp Cell Res 247: 208-219.
20. Viallard JF, Lacombe F, Dupouy M, Ferry H, Belloc F, et al. (2000) Different expression profiles of human cyclin B1 in normal PHA-stimulated T lymphocytes and leukemic T cells. Cytometry 39: 117-125.
21. Walker PMB, (1954) The Mitotic Index and Interphase Processes. J Exp Biol 31: 8-15.
22. Gray JW, Dolbeare F, Pallavicini MG, (1990) Quantitative cell-cycle analysis. In: Melamed MR, Lindmo T, Mendelsohn ML, editors. editors. Flow cytometry and cell sorting. Second ed. New York: Wiley-Liss.
23. Bagwell CB, (1993) Theoretical Aspects of Flow Cytometry Data Analysis. In: Bauer KD, Duque RE, Shankey TV, editors. editors. Clinical Flow Cytometry: principles and application. Baltimore: Williams & Wilkins.
24. Juan G, Traganos F, Darzynkiewicz Z, (1999) Histone H3 phosphorylation in human monocytes and during HL-60 cell differentiation. Exp Cell Res 246: 212-220.
25. Weis MC, (2011) Computational models of the mammalian cell cycle., Ph.D Thesis (Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland), 189.
26. Csikasz-Nagy A, (2009) Computational systems biology of the cell cycle. Brief Bioinform 10: 424-434.
27. Conradie R, Bruggeman FJ, Ciliberto A, Csikasz-Nagy A, Novak B, et al. (2010) Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. FEBS J 277: 357-367.
28. Becker M, Stolz A, Ertych N, Bastians H, (2010) Centromere localization of INCENP-Aurora B is sufficient to support spindle checkpoint function. Cell Cycle 9: 1360-1372.
29. Lozzio CB, Lozzio BB, (1973) Cytotoxicity of a factor isolated from human spleen. J Natl Cancer Inst 50: 535-538.
30. Jacobberger JW, Sramkoski RM, Frisa PS, Ye PP, Gottlieb MA, et al. (2003) Immunoreactivity of Stat5 phosphorylated on tyrosine as a cell-based measure of Bcr/Abl kinase activity. Cytometry A 54: 75-88.
31. Jacobberger JW, Fogleman D, Lehman JM, (1986) Analysis of intracellular antigens by flow cytometry. Cytometry 7: 356-364.
32. Jacobberger JW, Sramkoski RM, Stefan T, (2011) Multiparameter cell cycle analysis. Methods Mol Biol 699: 229-249.
33. Avva J, Weis MC, Soebiyanto RP, Jacobberger JW, Sreenath SN, (2011) CytoSys: a tool for extracting cell-cycle-related expression dynamics from static data. Methods Mol Biol 717: 171-193.