Poster Sessions

BIOINFO-22

Seth Johnson

S. Johnson, K. Camphausen, U. Shankavaram, S. Zhao

MAQuery: Radiation Oncology Microarray Expression Data Web Portal

Abundance of cancer research oriented portals is evident from a PubMed search, which returns over a thousand of abstracts. However, studies focusing strictly on Radiation effects on cancer are rare and to our knowledge there are no web portals dedicated to this topic. We have attempted to create a web portal called MAQuery that would house cancer related microarray expression data focusing primarily on radiation oncology data. MAQuery will help in search for genes with particular expression profiles in cancers that could be associated with radiation responsive genes when present and used as biomarkers, therapeutic target discovery, or validation. MAQuery consists of three broad modules: Genes, Cell Lines, and Arrays. Each module provides an entry point into the portal where search, comparison, and visualization can be accomplished. The portal revolves around gene oriented analysis and comparison. It houses extensive meta data relating to every existing human gene, such as gene pathways, Gene Ontology (GO) categories, PubMed reference id’s, other database cross-references, and location. This information is connected to microarray data through Gene Entrez ID. MAQuery also hosts metadata on cell lines that provides information about cancer lines that was used in microarray experiments. It consists of a single table providing background information such as source, patient’s demographics, histology, and references. Pre-processed microarray data consists of normalized expression values in log2 scale. Differential expression analysis was performed at each gene, sample, as well as tissue level for each microarray. This information will be presented in the query results for prioritization by the user. Gene module allows query by single or list of genes that will result in comparative analysis of the selected gene(s) across as many microarrays as the selection is present. Search by cell lines or arrays allow selecting from the list of cell lines or arrays in the database. Visualization of microarray studies’ comparisons is divided into two levels: comparisons within a microarray and comparisons between two different arrays. The former provides graphs and plots about how different tissues and tissue types respond to treatment, and the latter provides information on how common genes and cell lines perform based on different treatments.