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.

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Apr 10th, 12:00 PM Apr 10th, 1:00 PM

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.