Home LiteratureArticle Details
PMID: 11860205 Published · ppublish English Journal Article Review

Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium.

Plant molecular biology ·Vol. 48 ·No. 1-2 ·2002-01-00 ·Pages 119-31

Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S

Abstract

Genome-wide expression profiling with DNA microarrays has and will provide a great deal of data to the plant scientific community. However, reliability concerns have required the development data quality tests for common systematic biases. Fortunately, most large-scale systematic biases are detectable and some are correctable by normalization. Technical replication experiments and statistical surveys indicate that these biases vary widely in severity and appearance. As a result, no single normalization or correction method currently available is able to address all the issues. However, careful sequence selection, array design, experimental design and experimental annotation can substantially improve the quality and biological of microarray data. In this review, we discuss these issues with reference to examples from the Arabidopsis Functional Genomics Consortium (AFGC) microarray project.

MeSH Terms
Arabidopsis/genetics Genes, Plant/genetics Genetic Variation Genome, Plant Genomics Oligonucleotide Array Sequence Analysis/methods,standards Reproducibility of Results
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Finkelstein David
Carnegie Institution of Washington, Department of Plant Biology, Stanford, CA 94305, USA. [email protected]
Ewing Rob
Gollub Jeremy
Sterky Fredrik
Cherry J Michael
Somerville Shauna
References (51)
51 references, click to expand
  1. Various abiotic stresses rapidly activate Arabidopsis MAP kinases ATMPK4 and ATMPK6.
    Plant J. 2000 Dec;24(5):655-65 PMID: 11123804
  2. Identification of differentially expressed genes in human prostate cancer using subtraction and microarray.
    Cancer Res. 2000 Mar 15;60(6):1677-82 PMID: 10749139
  3. Statistical design and the analysis of gene expression microarray data.
    Genet Res. 2001 Apr;77(2):123-8 PMID: 11355567
  4. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library.
    Nat Genet. 1993 Aug;4(4):373-80 PMID: 8401585
  5. Microarray analysis of developing Arabidopsis seeds.
    Plant Physiol. 2000 Dec;124(4):1570-81 PMID: 11115875
  6. Normalization strategies for cDNA microarrays.
    Nucleic Acids Res. 2000 May 15;28(10):E47 PMID: 10773095
  7. Ratio-based decisions and the quantitative analysis of cDNA microarray images.
    J Biomed Opt. 1997 Oct;2(4):364-74 PMID: 23014960
  8. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations.
    Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9834-9 PMID: 10963655
  9. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
    Science. 1995 Oct 20;270(5235):467-70 PMID: 7569999
  10. Analysis of variance for gene expression microarray data.
    J Comput Biol. 2000;7(6):819-37 PMID: 11382364
  11. Generation of patterns from gene expression data by assigning confidence to differentially expressed genes.
    Bioinformatics. 2000 Aug;16(8):685-98 PMID: 11099255
  12. Array of hope for gene technology.
    Environ Health Perspect. 2001 Jan;109(1):A34-7 PMID: 11171543
  13. Gene expression data analysis.
    FEBS Lett. 2000 Aug 25;480(1):17-24 PMID: 10967323
  14. Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis.
    Plant Cell. 2000 May;12(5):707-20 PMID: 10810145
  15. Arabidopsis microarray service facilities.
    Plant Physiol. 2000 Dec;124(4):1468-71 PMID: 11115861
  16. d2_cluster: a validated method for clustering EST and full-length cDNAsequences.
    Genome Res. 1999 Nov;9(11):1135-42 PMID: 10568753
  17. The role of inorganic phosphate in the development of freezing tolerance and the acclimatization of photosynthesis to low temperature is revealed by the pho mutants of Arabidopsis thaliana.
    Plant J. 2000 Nov;24(3):383-96 PMID: 11069711
  18. Development of a prostate cDNA microarray and statistical gene expression analysis package.
    Mol Carcinog. 2000 May;28(1):12-22 PMID: 10820484
  19. Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets.
    In Silico Biol. 1999-2000;1(4):197-213 PMID: 11479934
  20. A concise guide to cDNA microarray analysis.
    Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556 passim PMID: 10997270
  21. One-stop shop for microarray data.
    Nature. 2000 Feb 17;403(6771):699-700 PMID: 10693778
  22. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2001 Jan 1;29(1):11-6 PMID: 11125038
  23. An ontology for biological function based on molecular interactions.
    Bioinformatics. 2000 Mar;16(3):269-85 PMID: 10869020
  24. Differential gene expression in Arabidopsis monitored using cDNA arrays.
    Plant J. 1998 Jun;14(5):643-52 PMID: 9675907
  25. Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis.
    Cell. 1990 Feb 9;60(3):357-64 PMID: 2302732
  26. JESAM: CORBA software components to create and publish EST alignments and clusters.
    Bioinformatics. 2000 Apr;16(4):313-25 PMID: 10869029
  27. Serial analysis of gene expression.
    Science. 1995 Oct 20;270(5235):484-7 PMID: 7570003
  28. The Stanford Microarray Database.
    Nucleic Acids Res. 2001 Jan 1;29(1):152-5 PMID: 11125075
  29. Alternative gene form discovery and candidate gene selection from gene indexing projects.
    Genome Res. 1998 Mar;8(3):276-90 PMID: 9521931
  30. Gene expression informatics--it's all in your mine.
    Nat Genet. 1999 Jan;21(1 Suppl):51-5 PMID: 9915502
  31. Expression monitoring by hybridization to high-density oligonucleotide arrays.
    Nat Biotechnol. 1996 Dec;14(13):1675-80 PMID: 9634850
  32. Chasing the dream: plant EST microarrays.
    Curr Opin Plant Biol. 2000 Apr;3(2):108-16 PMID: 10712953
  33. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.
    Genome Res. 2000 Dec;10(12):2030-43 PMID: 11116097
  34. Singular value decomposition for genome-wide expression data processing and modeling.
    Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10101-6 PMID: 10963673
  35. Mining the human genome using microarrays of open reading frames.
    Nat Genet. 2000 Nov;26(3):315-8 PMID: 11062470
  36. Microarray fabrication with covalent attachment of DNA using bubble jet technology.
    Nat Biotechnol. 2000 Apr;18(4):438-41 PMID: 10748527
  37. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
    Nucleic Acids Res. 2001 Jan 1;29(1):159-64 PMID: 11125077
  38. Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 PMID: 11309499
  39. On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data.
    J Comput Biol. 2001;8(1):37-52 PMID: 11339905
  40. A comparison of expressed sequence tags (ESTs) to human genomic sequences.
    Nucleic Acids Res. 1997 Apr 15;25(8):1626-32 PMID: 9092672
  41. Missing value estimation methods for DNA microarrays.
    Bioinformatics. 2001 Jun;17(6):520-5 PMID: 11395428
  42. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  43. STACK: Sequence Tag Alignment and Consensus Knowledgebase.
    Nucleic Acids Res. 2001 Jan 1;29(1):234-8 PMID: 11125101
  44. CAP3: A DNA sequence assembly program.
    Genome Res. 1999 Sep;9(9):868-77 PMID: 10508846
  45. Fundamental patterns underlying gene expression profiles: simplicity from complexity.
    Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8409-14 PMID: 10890920
  46. Dynamic modeling of gene expression data.
    Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1693-8 PMID: 11172013
  47. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples.
    Hum Mol Genet. 1999 Sep;8(9):1715-22 PMID: 10441335
  48. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.
    Science. 1999 Oct 15;286(5439):531-7 PMID: 10521349
  49. The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.
    Plant Physiol. 1996 Nov;112(3):1177-83 PMID: 8938416
  50. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array.
    Genome Res. 1996 Jun;6(6):492-503 PMID: 8828038
  51. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.
    Nucleic Acids Res. 2001 Jun 15;29(12):2549-57 PMID: 11410663
Article Info
Journal
Plant molecular biology
Abbr.
Plant Mol Biol
ISSN
0167-4412
DOI
10.1023/a:1013765922672
Email
[email protected]
Published
2002-01-00
Pages
119-31
Language
English
Region
Netherlands
NLM ID
9106343
Subset
IM
External Links
PubMed source DOI: 10.1023/a:1013765922672 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2