Dynamic querying for pattern identification in microarray and genomic data

TitleDynamic querying for pattern identification in microarray and genomic data
Publication TypeConference Proceedings
Year of Conference2003
AuthorsHochheiser H., Baehrecke E.H, Mount SM, Shneiderman B
Conference Name2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings
Date Published2003
ISBN Number0-7803-7965-9
KeywordsBioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher

Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.