Software and Methods for Oligonucleotide and CDNA Array Data Analysis

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2002 Jul 3

PMID 12093384

Citations 12

Authors

Matthew A Zapala

Daniel J Lockhart

Daniel G Pankratz

Anthony J Garcia

Carrolee Barlow

David J Lockhart

Affiliations

Soon will be listed here.

Abstract

Two HTML-based programs were developed to analyze and filter gene-expression data: 'Bullfrog' for Affymetrix oligonucleotide arrays and 'Spot' for custom cDNA arrays. The programs provide intuitive data-filtering tools through an easy-to-use interface. A background subtraction and normalization program for cDNA arrays was also built that provides an informative summary report with data-quality assessments. These programs are freeware to aid in the analysis of gene-expression results and facilitate the search for genes responsible for interesting biological processes and phenotypes.

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References

Coller H, Grandori C, Tamayo P, Colbert T, Lander E, Eisenman R . Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci U S A. 2000; 97(7):3260-5. PMC: 16226. DOI: 10.1073/pnas.97.7.3260. View

Bassett Jr D, Eisen M, Boguski M . Gene expression informatics--it's all in your mine. Nat Genet. 1999; 21(1 Suppl):51-5. DOI: 10.1038/4478. View

Sandberg R, Yasuda R, Pankratz D, Carter T, Del Rio J, Wodicka L . Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A. 2000; 97(20):11038-43. PMC: 27144. DOI: 10.1073/pnas.97.20.11038. View

Lockhart D, Barlow C . Expressing what's on your mind: DNA arrays and the brain. Nat Rev Neurosci. 2001; 2(1):63-8. DOI: 10.1038/35049070. View

Hughes T, Mao M, Jones A, Burchard J, Marton M, Shannon K . Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001; 19(4):342-7. DOI: 10.1038/86730. View

Miles M . Microarrays: lost in a storm of data?. Nat Rev Neurosci. 2001; 2(6):441-3. DOI: 10.1038/35077582. View

Carter T, Del Rio J, Greenhall J, Latronica M, Lockhart D, Barlow C . Chipping away at complex behavior: transcriptome/phenotype correlations in the mouse brain. Physiol Behav. 2001; 73(5):849-57. DOI: 10.1016/s0031-9384(01)00522-4. View

Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science. 1991; 251(4995):767-73. DOI: 10.1126/science.1990438. View

Farrant M, Feldmeyer D, Takahashi T, Cull-Candy S . NMDA-receptor channel diversity in the developing cerebellum. Nature. 1994; 368(6469):335-9. DOI: 10.1038/368335a0. View

10.

Zou L, Hagen S, Strait K, OPPENHEIMER J . Identification of thyroid hormone response elements in rodent Pcp-2, a developmentally regulated gene of cerebellar Purkinje cells. J Biol Chem. 1994; 269(18):13346-52. View

11.

Barlow C, Hirotsune S, Paylor R, Liyanage M, Eckhaus M, Collins F . Atm-deficient mice: a paradigm of ataxia telangiectasia. Cell. 1996; 86(1):159-71. DOI: 10.1016/s0092-8674(00)80086-0. View

12.

Shalon D, Smith S, Brown P . A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996; 6(7):639-45. DOI: 10.1101/gr.6.7.639. View

13.

Schena M, Shalon D, Heller R, Chai A, Brown P, Davis R . Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A. 1996; 93(20):10614-9. PMC: 38202. DOI: 10.1073/pnas.93.20.10614. View

14.

Derisi J, Penland L, Brown P, Bittner M, Meltzer P, Ray M . Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996; 14(4):457-60. DOI: 10.1038/ng1296-457. View

15.

Wodicka L, Dong H, Mittmann M, Ho M, Lockhart D . Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol. 1998; 15(13):1359-67. DOI: 10.1038/nbt1297-1359. View

16.

Lockhart D, Dong H, Byrne M, Follettie M, Gallo M, Chee M . Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996; 14(13):1675-80. DOI: 10.1038/nbt1296-1675. View

17.

Lipshutz R, Fodor S, Gingeras T, Lockhart D . High density synthetic oligonucleotide arrays. Nat Genet. 1999; 21(1 Suppl):20-4. DOI: 10.1038/4447. View

18.

Brown P, Botstein D . Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999; 21(1 Suppl):33-7. DOI: 10.1038/4462. View

19.

Debouck C, Goodfellow P . DNA microarrays in drug discovery and development. Nat Genet. 1999; 21(1 Suppl):48-50. DOI: 10.1038/4475. View

20.

Lockhart D, Winzeler E . Genomics, gene expression and DNA arrays. Nature. 2000; 405(6788):827-36. DOI: 10.1038/35015701. View