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 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.
Mattes
William B
WB
Investigative Toxicology, Pfizer Inc, Kalamazoo, Michigan, USA. wmattes@genelogic.com
D000465:Algorithms; D000818:Animals; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D006801:Humans; D016247:Information Storage and Retrieval; D009696:Nucleic Acids; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*
D009696:Nucleic Acids