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

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 th...

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Detalles Bibliográficos
Autor principal: Mattes, William B
Formato: Texto
Lenguaje:English
Publicado: 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241905/
https://www.ncbi.nlm.nih.gov/pubmed/15033601
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author Mattes, William B
author_facet Mattes, William B
author_sort Mattes, William B
collection PubMed
description 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.
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spelling pubmed-12419052005-11-08 Annotation and cross-indexing of array elements on multiple platforms. Mattes, William B Environ Health Perspect Research Article 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. 2004-03 /pmc/articles/PMC1241905/ /pubmed/15033601 Text en
spellingShingle Research Article
Mattes, William B
Annotation and cross-indexing of array elements on multiple platforms.
title Annotation and cross-indexing of array elements on multiple platforms.
title_full Annotation and cross-indexing of array elements on multiple platforms.
title_fullStr Annotation and cross-indexing of array elements on multiple platforms.
title_full_unstemmed Annotation and cross-indexing of array elements on multiple platforms.
title_short Annotation and cross-indexing of array elements on multiple platforms.
title_sort annotation and cross-indexing of array elements on multiple platforms.
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241905/
https://www.ncbi.nlm.nih.gov/pubmed/15033601
work_keys_str_mv AT matteswilliamb annotationandcrossindexingofarrayelementsonmultipleplatforms