Skip to main content
NCBI home page
Environmental Health Perspectives logoLink to Environmental Health Perspectives
. 2004 Mar;112(4):506–510. doi: 10.1289/ehp.6698

Annotation and cross-indexing of array elements on multiple platforms.

William B Mattes 1
PMCID: PMC1241905  PMID: 15033601

Abstract

On the surface, transcript profiling using microarrays seems to offer a way of looking at the global response of the cell to perturbation, with a focus on changes in gene expression. The difficulty, however, is that the response of a particular gene is actually measured on the array by an element that is a short, defined nucleic acid sequence. Sequences that map back to the same genetic locus may actually be given different names and descriptions when they are deposited in public sequence databases; when such sequences are used in microarray construction, elements that monitor the same genetic locus may have different names and descriptions. The algorithm described here uses a hierarchical approach to assign a single best annotation to the elements in a given microarray in such a fashion that elements from one microarray platform may be cross-indexed with those of another. The algorithm relies on the nucleic acid accession number for a given array element, and uses that to retrieve annotation from the most recent versions of LocusLink and UniGene. Both database resources are searched, with a priority being given to annotation derived from the curated LocusLink database. In lieu of annotation found in these databases, the default GenBank annotation is used. As a final outcome, a cross-chip identifier is generated that may be used to cross-index array elements. The program is available as a practical extraction and report language (Perl) script that can run under any Perl interpreter.

Full Text

The Full Text of this article is available as a PDF (132.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25–29. doi: 10.1038/75556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bouton C. M., Pevsner J. DRAGON: Database Referencing of Array Genes Online. Bioinformatics. 2000 Nov;16(11):1038–1039. doi: 10.1093/bioinformatics/16.11.1038. [DOI] [PubMed] [Google Scholar]
  3. Chao K. M., Pearson W. R., Miller W. Aligning two sequences within a specified diagonal band. Comput Appl Biosci. 1992 Oct;8(5):481–487. doi: 10.1093/bioinformatics/8.5.481. [DOI] [PubMed] [Google Scholar]
  4. Kokame K., Kato H., Miyata T. Homocysteine-respondent genes in vascular endothelial cells identified by differential display analysis. GRP78/BiP and novel genes. J Biol Chem. 1996 Nov 22;271(47):29659–29665. doi: 10.1074/jbc.271.47.29659. [DOI] [PubMed] [Google Scholar]
  5. Liu Guoying, Loraine Ann E., Shigeta Ron, Cline Melissa, Cheng Jill, Valmeekam Venu, Sun Shaw, Kulp David, Siani-Rose Michael A. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003 Jan 1;31(1):82–86. doi: 10.1093/nar/gkg121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Mattes William B., Pettit Syril D., Sansone Susanna-Assunta, Bushel Pierre R., Waters Michael D. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004 Mar;112(4):495–505. doi: 10.1289/ehp.6697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Mattes William B., Pettit Syril D., Sansone Susanna-Assunta, Bushel Pierre R., Waters Michael D. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004 Mar;112(4):495–505. doi: 10.1289/ehp.6697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Pruitt K. D., Maglott D. R. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 2001 Jan 1;29(1):137–140. doi: 10.1093/nar/29.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Thompson Karol L., Afshari Cynthia A., Amin Rupesh P., Bertram Timothy A., Car Bruce, Cunningham Michael, Kind Clive, Kramer Jeffrey A., Lawton Michael, Mirsky Michael. Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. Environ Health Perspect. 2004 Mar;112(4):488–494. doi: 10.1289/ehp.6676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Wain H., White J., Povey S. The changing challenges of nomenclature. Cytogenet Cell Genet. 1999;86(2):162–164. doi: 10.1159/000015372. [DOI] [PubMed] [Google Scholar]
  11. Wheeler D. L., Chappey C., Lash A. E., Leipe D. D., Madden T. L., Schuler G. D., Tatusova T. A., Rapp B. A. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2000 Jan 1;28(1):10–14. doi: 10.1093/nar/28.1.10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. White J., Wain H., Bruford E., Povey S. Promoting a standard nomenclature for genes and proteins. Nature. 1999 Nov 25;402(6760):347–347. doi: 10.1038/46405. [DOI] [PubMed] [Google Scholar]
  13. Zhong Sheng, Li Cheng, Wong Wing Hung. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3483–3486. doi: 10.1093/nar/gkg598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Zhou D., Salnikow K., Costa M. Cap43, a novel gene specifically induced by Ni2+ compounds. Cancer Res. 1998 May 15;58(10):2182–2189. [PubMed] [Google Scholar]
  15. van Belzen N., Dinjens W. N., Diesveld M. P., Groen N. A., van der Made A. C., Nozawa Y., Vlietstra R., Trapman J., Bosman F. T. A novel gene which is up-regulated during colon epithelial cell differentiation and down-regulated in colorectal neoplasms. Lab Invest. 1997 Jul;77(1):85–92. [PubMed] [Google Scholar]

Articles from Environmental Health Perspectives are provided here courtesy of National Institute of Environmental Health Sciences

RESOURCES