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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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Formato: | Texto |
Lenguaje: | English |
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2004
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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. |
format | Text |
id | pubmed-1241905 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2004 |
record_format | MEDLINE/PubMed |
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 |