A regression model approach to enable cell morphology correction in high-throughput flow cytometry

Molecular Systems Biology

Volumn 7, Issue , 2011, Pages

  Knijnenburg, Theo A ^a,c   Roda, Oriol ^a,c   Wan, Yakun ^a   Nolan, Garry P ^b   Aitchison, John D ^a,d   Shmulevich, Ilya ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b STANFORD UNIVERSITY   (United States)

^c NETHERLANDS CANCER INSTITUTE   (Netherlands)

^d SOUTHEAST UNIVERSITY   (China)

Author keywords

flowcytometry; high throughput experiments; statistical regressionmodel; transcriptional noise

Indexed keywords

GALACTOSE; GLUCOSE; GREEN FLUORESCENT PROTEIN; NUCLEOPORIN; OLEIC ACID; TELOMERE BINDING PROTEIN;

ARTICLE; CELL GRANULE; CELL HETEROGENEITY; CELL SIZE; CELL STRUCTURE; CONTROLLED STUDY; FLOW CYTOMETRY; FLUORESCENCE ANALYSIS; PRIORITY JOURNAL; STATISTICAL ANALYSIS; CYTOLOGY; DRUG EFFECT; EPIGENETICS; FLUORESCENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SCREENING; METABOLISM; METHODOLOGY; MUTATION; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL; STATISTICS; TRANSGENIC ORGANISM;

CELL SIZE; EPIGENOMICS; FLOW CYTOMETRY; FLUORESCENCE; GENETIC VARIATION; GLUCOSE; GREEN FLUORESCENT PROTEINS; HIGH-THROUGHPUT SCREENING ASSAYS; MODELS, STATISTICAL; MUTATION; NUCLEAR PORE COMPLEX PROTEINS; OLEIC ACID; ORGANISMS, GENETICALLY MODIFIED; SACCHAROMYCES CEREVISIAE; TELOMERE-BINDING PROTEINS; TRANSCRIPTION, GENETIC;

EID: 80053404632     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.64     Document Type: Article

References (34)

1. Acar M, Mettetal JT, van Oudenaarden A (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471-475 (Pubitemid 351450880)
2. Batenchuk C, St-Pierre S, Tepliakova L, Adiga S, Szuto A, Kabbani N, Bell JC, Baetz K, Kærn M (2011) Chromosomal position effects are linked to sir2-mediated variation in transcriptional burst size. Biophys J 100: L56
3. Botev Z, Grotowski J, Kroese D (2010) Kernel density estimation via diffusion. Ann Stat 38: 2916-2957
4. Brickner DG, Cajigas I, Fondufe-Mittendorf Y, Ahmed S, Lee PC, Widom J, Brickner JH (2007) H2A. Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 5: E81
5. Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, Buc H, Feuerbach-Fournier F, Olivo-Marin JC, Hurt EC, Nehrbass U (2006) SAGA interacting factors confine subdiffusion of transcribed genes to the nuclear envelope. Nature 441: 770-773 (Pubitemid 43865225)
6. Cagatay T, Turcotte M, Elowitz MB, Garcia-Ojalvo J, Suel GM (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139: 512-522
7. Capelson M, Liang Y, Schulte R, MairW,Wagner U, HetzerMW(2010) Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 140: 372-383
8. Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA (2004) Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117: 427-439 (Pubitemid 38610229)
9. Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD (2005) The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. J Cell Biol 171: 955
10. Einerhand AW, Voorn-Brouwer TM, Erdmann R, Kunau WH, Tabak HF (1991) Regulation of transcription of the gene coding for peroxisomal 3-oxoacyl-CoA thiolase of Saccharomyces cerevisiae. Eur J Biochem 200: 113-122
11. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186 (Pubitemid 36193353)
12. Galy V, Olivo-Marin JC, Scherthan H, Doye V, Rascalou N, Nehrbass U (2000) Nuclear pore complexes in the organization of silent telomeric chromatin. Nature 403: 108-112 (Pubitemid 30038531)
13. Igual JC, Gonzalez-Bosch C, Franco L, Perez-Ortin JE (1992) The POT1 gene for yeast peroxisomal thiolase is subject to three different mechanisms of regulation. Mol Microbiol 6: 1867-1875
14. Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK (2002) Chromatin boundaries in budding yeast: The nuclear pore connection. Cell 109: 551-562 (Pubitemid 34628719)
15. Kalverda B, Pickersgill H, Shloma VV, FornerodM(2010) Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 140: 360-371
16. Krutzik P, Nolan G (2006) Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling. Nat Methods 3: 361
17. Lo K, Brinkman RR, Gottardo R (2008) Automated gating of flow cytometry data via robust model-based clustering. Cytometry A 73: 321-332 (Pubitemid 351522115)
18. Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526-529 (Pubitemid 47196119)
19. Menon BB, Sarma NJ, Pasula S, Deminoff SJ, Willis KA, Barbara KE, Andrews B, Santangelo GM (2005) Reverse recruitment: The Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc Natl Acad Sci USA 102: 5749-5754 (Pubitemid 40559631)
20. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840-846
21. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A (2002) Regulation of noise in the expression of a single gene. Nat Genet 31: 69-73
22. Pyne S, Hu X, Wang K, Rossin E, Lin TI, Maier LM, Baecher-Allan C, McLachlan GJ, Tamayo P, Hafler DA, De Jager PL, Mesirov JP (2009) Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci USA 106: 8519-8524
23. Raj A, van Oudenaarden A (2008) Nature, nurture, or chance: Stochastic gene expression and its consequences. Cell 135: 216-226
24. Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD (2006) Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38: 1082-1087 (Pubitemid 44325937)
25. Raser JM, O'Shea EK (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814 (Pubitemid 38787899)
26. Ratushny AV, Ramsey SA, RodaO,Wan Y, Smith JJ, Aitchison JD (2008) Control of transcriptional variability by overlapping feed-forward regulatory motifs. Biophys J 95: 3715-3723
27. Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD (2008) Genomewide analysis of signaling networks regulating fatty acidinduced gene expression and organelle biogenesis. J Cell Biol 181: 281-292 (Pubitemid 351574553)
28. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22: 1567-1572 (Pubitemid 40039460)
29. Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD (2006) Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Mol Syst Biol 2: 2006.0009
30. Song C, Phenix H, Abedi V, Scott M, Ingalls BP, Kaern M, Perkins TJ (2010) Estimating the stochastic bifurcation structure of cellular networks. PLoS Comput Biol 6: E1000699
31. Straube K, Blackwell Jr J, Pemberton L (2010) Nap1 and Chz1 have separate Htz1 nuclear import and assembly functions. Traffic 11: 185-197
32. Suel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz MB (2007) Tunability and noise dependence in differentiation dynamics. Science 315: 1716-1719 (Pubitemid 46515626)
33. Wan Y, Saleem R, Ratushny A, Roda O, Smith J, Lin CH, Chiang JH, Aitchison J (2009) The role of the histone variant H2A.Z/Htz1p on TBP recruitment, chromatin dynamics and regulated expression at oleate-responsive genes. Mol Cell Biol 29: 2346-2358
34. Wu WH, Wu CH, Ladurner A, Mizuguchi G, Wei D, Xiao H, Luk E, Ranjan A, Wu C (2009) N terminus of Swr1 binds to histone H2AZ and provides a platform for subunit assembly in the chromatin remodeling complex. J Biol Chem 284: 6200-6207.