A rapid method for computationally inferring transcriptome coverage and microarray sensitivity

Bioinformatics

Volumn 21, Issue 1, 2005, Pages 80-89

  Reverter, A ^a   McWilliam, S M ^a   Barris, W ^a   Dalrymple, B P ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA; OLIGONUCLEOTIDE; TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CATTLE; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC TRANSCRIPTION; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; SAMPLING; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION; SHEEP; TECHNOLOGY;

EID: 12344315892     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth472     Document Type: Article

References (38)

1. Berthier,D., Quéré,R., Thevenon,S., Belemsaga,E., Piquemal,D., Marti,J. and Maillard,J.-C. (2003) Serial analysis of gene expression (SAGE) in bovine trypanotolerance: preliminary results. Genet. Sel. Evol., 35(Suppl. 1), S35-S47.
2. Bickel,D.R. (2004) Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes. Bioinformatics, 20, 682-688.
3. Brenner,S., Johnson,M., Bridgham,J., Golda,G., Lloyd,D.H., Johnson,D., Luo,S., McCurdy,S., Foy,M., Ewan,M. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630-634.
4. Brown,E.N., McDermott,T.J., Bloch,K.J. and McCollom,A.D. (1996) Defining the smallest analyte concentration an immunoassay can measure. Clinical Chem., 42, 893-903.
5. Callow,M.J., Dudoit,S., Gong,E.L., Speed,T.P. and Rubin,E.M. (2000) Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Res., 10, 2022-2029.
6. Chudin,E., Walker,R., Kosaka,A., Wu,S.X., Rabert,D., Chang,T.K. and Kreder,D.E. (2001) Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip® arrays. Genome Biol., 3, research0005.1-research0005.10.
7. Dror,R.O., Murnick,J.G., Rinaldi,N.J., Marinescu,V.D., Rifkin,R.M. and Young,R.A. (2003) Bayesian estimation of transcript level using a general model of array measurement noise. J. Comput. Biol., 10, 433-452.
8. Dudley,A.M., Aach,J., Steffen,M.A. and Church,G.M. (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl Acad Sci. USA, 99, 7554-7559.
9. Everitt,B.S. (2002) The Cambridge Dictionary of Statistics 2nd edn. Cambridge University Press, Cambridge, UK.
10. Hanley,J.A. and McNeil,B.J. (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29-36.
11. Hawken,R.J., Barris,W.C., McWilliam,S. and Dalrymple,B.P. (2004) An Interactive Bovine In silico SNP database (IBISS). Mamm. Genome, 15, 819-827.
12. Heagerty,P.J., Lumley,T. and Pepe,M. (2000) Time dependent ROC curves for censored survival data and a diagnostic marker. Biometrics, 56, 337-344.
13. Hraber,P.T. (2001) Discovering molecular mechanisms of mutualism with computational approaches to endosymbiosis. PhD Dissertation, University of New Mexico, Albuquerque, NM, USA.
14. Ishii,M., Hashimoto,S., Tsutsumi,S., Wada,Y., Matsushima,K., Kodama,T. and Aburatani,H. (2000) Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics, 68, 136-143.
15. Jongeneel,C.V., Iseli,C., Stevenson,B.J., Riggins,G.J., Lal,A., Mackay,A., Harris,R.A., O'Hare,M.J., Neville,A.M., Simpson,A.J. and Strausberg,R.L. (2003) Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc. Natl Acad. Sci. USA, 100, 4702-4705.
16. Kane,M.D., Jatkoe,T.A., Stumpf,C.R., Lu,J., Thomas,J.D. and Madore,S.J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res., 28, 4552-4557.
17. Kuznetsov,V.A. (2001) Distribution associated with stochastic processes of gene expression in a single eukaryotic cell EURASIP. J. Appl. Signal Proc., 4, 285-296.
18. Kuznetsov,V.A., Knott,G.D. and Bonner,R.F. (2002) General statistics of stochastic process of gene expression in eukaryotic cells. Genetics, 161, 1321-1332.
19. Lash,A.E., Tolstoshev,C.M., Wagner,L., Schuler,G.D., Strausberg,R.L., Riggins,G.J. and Altschul,F. (2000) SAGEmap: a public gene expression resource. Genome Res., 10, 1051-1060.
20. Lee,H.S., Wang,J., Tian,L., Jiang,H., Black,M.A., Madlung,A., Watson,B., Lukens,L., Pires,J.C., Wang,J.J. et al. (2004) Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnol. J., 2, 45-52.
21. Lemon,W.J., Liyanarachchi,S. and You,M. (2003) A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol., 4, R67.
22. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
23. Li,H. and Gui,J. (2004) Partial Cox regression analysis for high-dimensional microarray gene expression data. Bioinformatics, 20(Suppl. 1), i208-i215.
24. Lin,J.Y., Pollack,J.R., Chou,F.L., Rees,C.A., Christian,A.T., Bedford,J.S., Brown,P.O. and Ginsberg,M.H. (2002) Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays. Genome Biol., 3, research0026.1-research0026.7.
25. Lockhart,D.J. and Winzeler,E.A. (2000) Genomics, gene expression, and DNA arrays. Nature, 405, 827-836.
26. Meissner,N., Radke,J., Hedges,J.F., White,M., Behnke,M., Bertolino,S., Mitchell,A. and Jutila,M.A. (2003) Serial analysis of gene expression in circulating γδ T cell subsets defines distinct immunoregulatory phenotypes and unexpected gene expression profiles. J. Immunol., 170, 356-364.
27. Miller,R.T., Christoffels,A.G., Gopalakrishnan,C., Burke,J., Ptitsyn,A.A, Broveak,T.R. and Hide,W.A. (1999) A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base. Genome Res., 11, 1143-55.
28. Morris,J.S., Baggerly,K.A. and Coombes,K.R. (2003) Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. Biometrics, 59, 476-486.
29. Neill,J.D. and Ridpath,J.F. (2003) Gene expression changes in BVDV2-infected MDBK cells. Biologicals, 31, 97-102.
30. Nicholson,W. (1985) Microeconomic Theory: Basic Principles and Extensions, 3rd edn. The Dryden Press, New York.
31. O'Malley,A.J. and Deely,J.J. (2003) Bayesian measures of the minimum detectable concentration of an immunoassay. Aust. N. Z. J. Stat., 45, 43-65.
32. Pepe,M.S., Longton,G., Anderson,G.L. and Schummer,M. (2003) Selecting differentially expressed genes from microarray experiments. Biometrics, 59, 133-142.
33. Tu,Y., Stolovitzky,G. and Klein,U. (2002) Quantitative noise analysis for gene expression microarray experiments. Proc. Natl Acad. Sci., USA, 99, 14031-14036.
34. Ueda,H.R., Hayashi,S., Matsuyama,S., Yomo,T., Hashimoto,S., Kay,S.A., Hogenesch,J.B. and Lino,M. (2004) Universality and flexibility in gene expression from bacteria to human. Proc. Natl Acad. Sci., USA 101, 3765-3769.
35. Velculescu,V.E., Zhang,L., Vogelstein,B. and Kinzler,K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
36. Velculescu,V.E., Zhang,L., Zhou,W., Vogelstein,J. Basrai,M.A., Bassett,E.E., Hieter,P., Vogelstein,B. and Kinzler,K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
37. Wang,H., Hubbell,E., Hu,J., Mei,G., Cline,M., Lu,G., Clark,T., Siani-Rose,M.A., Ares,M., Kulp,D.C. and Haussler,D. (2003) Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics, 19(Supp. 1), i315-i322.
38. Zien,A., Fluck,J., Zimmer,R. and Lengauer,T. (2003) Microarrays: how many do you need? J. Comput. Biol., 10, 653-667.