Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases.
The increasing popularity of DNA chip technology for the study of gene expression is producing, for each experiment, a sizable quantity of numerical data to analyse and an accompanying large number of gene identifiers that should be associated with the relevant biological annotation. We describe here a website at IFOM (FIRC Institute of Molecular Oncology) where we release regularly updated annotation tables for the most used Affymetrix oligonucleotide DNA chips and for the whole Research Genetics 46K clone collection for cDNA arrays. These tables are synchronised with every new release of the mouse and human UniGene databases (NCBI; National Center for Biotechnology Information), allowing fast and easy preliminary annotation of DNA array experiments. We also report some comparative evidence about the importance of biological database synchronisation and cross-references in the process of generating annotation tables for DNA chips.
Guffanti
Alessandro
A
FIRC Institute of Molecular Oncology, Milan, Italy. guffanti@ifom-firc.it
Finocchiaro
Giacomo
G
Reid
James F
JF
Luzi
Lucilla
L
Alcalay
Myriam
M
Confalonieri
Stefano
S
Lassandro
Lelio
L
Muller
Heiko
H
D000043:Abstracting and Indexing / Q000379:methods*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D009317:National Library of Medicine (U.S.); D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014481:United States