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Visualization tool for data analysis

Visualization tool for data analysis. Uma Chandran, PhD Department of Biomedical Informatics 1/11/2013. Research Questions. Gene expression signatures of estrogen response in breast versus bone versus endometrium

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Visualization tool for data analysis

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  1. Visualization tool for data analysis Uma Chandran, PhD Department of Biomedical Informatics 1/11/2013

  2. Research Questions • Gene expression signatures of estrogen response in breast versus bone versus endometrium • Experimental system could be cell cultures treated at various time points with estrogen or vehicle alone • Extract RNA, perform microarray experiments and analyze data • Not all data can be generated in-house • So, in-house and publicly available data

  3. Data analysis • Data • Platforms such as Affymetrix expression arrays, • Generate data in-house or download from databases such as GEO • Analysis • Compare gene expression profiles between various classes, for example, hormone treated v hormone naïve • Data analysis in R either through GEO or by us • Outputs • Excel spreadsheets, many comparisons, many work sheets

  4. Challenges • Interaction with databases • Downloads, data analysis • Numerous Excel spreadsheets • Not an easy way for end-users to compare results • Example: In how many data sets is MUC1 differentially expressed? How many genes from a user-defined gene list is differentially expressed in a particular study? • Numerous portals such as GEO, Array Express, cBIO are examples of visualization interfaces • We need something similar but much smaller scale for our own analysis results so that end-user can manipulate data easily

  5. Tasks • Download data from multiple studies • Develop pipeline for analysis in R • Output results to a database • Simple visualization where user can input gene id, gene list or select study from dropdown • Output as expression values, p values etc

  6. Team Mentors • Uma Chandran, PhD – Requirements, data analysis, R • Xinghua Lu, MD, PhD – Data analysis • Harry Hochheiser, PhD – Database technologies, programming

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