Event Title
A Web Interface to Search for Similar Temporal Gene Expression Profiles - Implementation and Use
Presentation Type
Poster/Portfolio
Presenter Major(s)
Computer Information Systems, Finance, Medical and BioInformatics
Mentor Information
Guenter Tusch
Department
School of Computing and Information Systems
Location
Kirkhof Center KC8
Start Date
10-4-2013 12:00 PM
End Date
10-4-2013 1:00 PM
Keywords
Information, Innovation, and Technology, Life Science
Abstract
PURPOSE: Advances in microarray technology have led to highly complex datasets often addressing similar or related biological questions. Molecular biological research is often based on measurements that have been obtained at different points in time. The biologist looks at these values not as individual points, but as a progression over time. Our program (SPOT) helps the researcher find these patterns in large sets of microarray data. PROCEDURES: A researcher proceeds through three subsequent steps: first, selection of microarray data of interesting experiments from a public functional genomics data repository, NCBI GEO, second, translating the temporal measurements into time intervals, and third, defining temporal concepts like peaks based on those intervals. OUTCOME: We created a software tool using open-source platforms supporting the R statistical package, PHP, Bioconductor, and Protege-OWL. The poster focuses on use of the interface and challenges of using public databases.
A Web Interface to Search for Similar Temporal Gene Expression Profiles - Implementation and Use
Kirkhof Center KC8
PURPOSE: Advances in microarray technology have led to highly complex datasets often addressing similar or related biological questions. Molecular biological research is often based on measurements that have been obtained at different points in time. The biologist looks at these values not as individual points, but as a progression over time. Our program (SPOT) helps the researcher find these patterns in large sets of microarray data. PROCEDURES: A researcher proceeds through three subsequent steps: first, selection of microarray data of interesting experiments from a public functional genomics data repository, NCBI GEO, second, translating the temporal measurements into time intervals, and third, defining temporal concepts like peaks based on those intervals. OUTCOME: We created a software tool using open-source platforms supporting the R statistical package, PHP, Bioconductor, and Protege-OWL. The poster focuses on use of the interface and challenges of using public databases.