Whole-genome microarrays of fission yeast: Characteristics, accuracy, reproducibility, and processing of array data

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Lyne, Rachel ^a,b   Burns, Gavin ^a   Mata, Juan ^a   Penkett, Chris J ^a   Rustici, Gabriella ^a   Chen, Dongrong ^a   Langford, Cordelia ^a   Vetrie, David ^a   Bähler, Jürg ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FLUOROCHROME; FLUORESCENT DYE; PRIMER DNA;

ACCURACY; ARTICLE; ARTIFACT; CONTROLLED STUDY; COVALENT BOND; CROSS HYBRIDIZATION; DATA ANALYSIS; DNA MICROARRAY; FLUORESCENCE; FUNGAL GENE; GENE SEQUENCE; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; MOLECULAR PROBE; NONHUMAN; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SAMPLE; SCHIZOSACCHAROMYCES POMBE; SIGNAL PROCESSING; EVALUATION; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; SCHIZOSACCHAROMYCES;

SCHIZOSACCHAROMYCES POMBE;

DNA PRIMERS; FLUORESCENT DYES; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SCHIZOSACCHAROMYCES;

EID: 9144229663     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-27     Document Type: Article

References (42)

1. Brown PO and Botstein D: Exploring the new world of the genome with DNA microarrays Nat Genet 1999, Suppl 21: 3-37.
2. Lockhart D and Winzeler E: Genomics, gene expression and DNA arrays Nature 2000, 405:827-836.
3. Young R: Biomedical discovery with DNA arrays Cell 2000, 102:9-16.
4. Schena M, Shalon D, Davis RW and Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995, 270:467-470.
5. Shalon D, Smith SJ and Brown PO: A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization Genome Res 1996, 6:639-645.
6. Churchill GA: Fundamentals of experimental design for cDNA microarrays Nat Genet 2002, 32(Suppl 2):490-495.
7. Holloway AJ, Van Laar RK, Tothill RW and Bowtell DD: Options available-from start to finish-for obtaining data from DNA microarrays II Nat Genet 2002, 32(Suppl 2):481-489.
8. Quackenbush J: Microarray data normalization and transformation Nat Genet 2002, 32(Suppl 2):496-501.
9. Yang YH and Speed T: Design issues for cDNA microarray experiments Nat Rev Genet 2002, 3:579-588.
10. Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J and Baker S et al.: The genome sequence of Schizosaccharomyces pombe Nature 2002, 415: 71-880.
11. Schizosaccharomyces pombe GeneDB [http://www.genedb.org/genedb/pombe/index.jsp]
12. Wood V and Bähler J: How to get the best from fission yeast genome data Comp Funct Genom 2002, 3:282-288.
13. Delneri D, Branca FL and Oliver SG: Towards a truly intergrative biology through the functional genomics of yeast Curr Opin Biotechnol 2001, 12:87-91.
14. Kumar A and Snyder M: Emerging technologies in yeast genomics Nat Rev Genet 2001, 2:302-312.
15. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL and Hedges SB: Molecular evidence for the early colonization of land by fungi and plants Science 2001, 293:1129-1133.
16. Mata J, Lyne R, Burns G and Bähler J: The transcriptional program of meiosis and sporulation in fission yeast Nat Genet 2002, 32:143-147.
17. Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N and Bähler J: Global transcriptional responses of fission yeast to environmental stress Mol Biol Cell 2003, 14: 14-229.
18. Stillman BA and Tonkinson JL: Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate Anal Biochem 2001, 295:149-157.
19. Franssen-van Hal NL, Vorst O, Kramer E, Hall RD and Keijer J: Factors influencing cDNA microarray hybridization on silylated glass slides Anal Biochem 2002, 308:5-17.
20. Perez-Hidalgo L, Moreno S and San-Segundo PA: Regulation of meiotic progression by the meiosis-specific checkpoint kinase Mek1 in fission yeast J Cell Sci 2003, 116:259-271.
21. Molnar M, Parisi S, Kakihara Y, Nojima H, Yamamoto A, Hiraoka Y, Bozsik A, Sipiczki M and Kohli J: Characterization of rec7, an early recombination gene in Schizosaccharomyces pombe. Genetics 2001, 157:519-532.
22. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J and Li J et al.: Within the fold: assessing differential expression measures and reproducibility in microarray assays Genome Biol 2002, 3:research0062.
23. Yang YH and Speed T: Representing and evaluating slide data In DNA Microarrays Edited by: Bowtell D, Sambrook J. New York: Cold Spring Harbor Laboratory Press; 2002:544-551.
24. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J and Speed TP: Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30:e15.
25. Verdnik D, Handran S and Pickett S: Key considerations for accurate microarray scanning and image analysis In: DNA Array Image Analysis: Nuts & Bolts Edited by: Kamberova G, Shishir S. DNA Press LLC; 2002:83-98.
26. Colantuoni C, Henry G, Zeger S and Pevsner J: Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts Biotechniques 2002, 32:1316-1320.
27. Snijders AM, Meijer GA, Brakenhoff RH, van den Brule AJC and van Diest PJ: Microarray techniques in pathology: tool or toy? Mol Pathol 2000, 53:289-294.
28. Tusher VG, Tibshirani R and Chu G: Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci USA 2001, 98:5116-5121.
29. Bähler Lab Website: Pombe Functional Genomics [http://www.sanger.ac.uk/PostGenomics/S_pombe/]
30. Rozen S and Skaletsky HJ: Primer3 on the WWW for general users and for biologist programmers In: Bioinformatics Methods and Protocols: Methods in Molecular Biology Edited by: Krawetz S, Misener S, Totowa NJ. Humana Press; 2000:365-386.
31. Primer3 Code [http://www-genome.wi.mit.edu/genome_software/other/primer3.html]
32. Watanabe T, Miyashita K, Saito TT, Nabeshima K and Nojima H: Abundant Poly(A)-bearing RNAs that lack open reading frames in Schizosacharomyces pombe. DNA Research 2002, 9:209-215.
33. Bähler J, Wu JQ, Longtine MS, Shah NG, McKenzie A III, Steever AB, Wach A, Philippsen P and Pringle JR: Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe Yeast 1998, 14:943-951.
34. Tasto JJ, Carnahan RH, McDonald WH and Gould KL: Vectors and gene targeting modules for tandem affinity purification in Schizosaccharomyces pombe Yeast 2001, 18:657-662.
35. Craven RA, Griffiths DJ, Sheldrick KS, Randall RE, Hagan IM and Carr AM: Vectors for the expression of tagged proteins in Schizosaccharomyces pombe Gene 1998, 221:59-68.
36. The Microarray Facility at the Sanger Institute [http://www.sanger.ac.uk/Projects/Microarrays/]
37. Watanabe T, Miyashita K, Saito TT, Yoneki T, Kakihara Y, Nabeshima K, Kishi YA, Shimoda C and Nojima H: Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe Nucleic Acids Res 2001, 29:2327-2337.
38. Fikes JD, Becker DM, Winston F and Guarente L: Striking conservation of TFIID in Schizosaccharomyces pombe and Saccharomyces cerevisiae Nature 1990, 346:291-294.
39. Leupold U: Genetical methods for Schizosaccharomyces pombe Meth Cell Physiol 1970, 4:169-177.
40. Fission Yeast Handbook [http://www.sanger.ac.uk/PostGenomics/S_ppmbe/docs/nurse_lad_manual.pdf]
41. Brody JP, Williams BA, Wold BJ and Quake SR: Significance and statistical errors in the analysis of DNA microarray data Proc Natl Acad Sci USA 2002, 99:12975-12978.
42. + encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA Cell 1994, 78:487-498.