DIMACS Short Course: Gene Expression Resources at the National Center for Biotechnology Information (NCBI)

Speaker: Susan M. Dombrowski, Ph.D., NCBI

April 13 - 14, 2004
DIMACS Center, CoRE Building, Rutgers University

Organizers:

Paul Ehrlich, BIOMAPS Institute, pehrlich@biomaps.rutgers.edu

Mel Janowitz, DIMACS, melj@dimacs.rutgers.edu

Tara Matise, Department of Genetics, matise@biology.rutgers.edu

Intended Audience

This course is intended for principal investigators, senior scientists, thesis directors, laboratory directors, postdoctoral fellows, graduate students, advanced undergraduates and scientific support staff who would like to incorporate gene expression data into their research.

Course Summary and Objectives

The training course presented by the NCBI is a 1 ½ hour lecture and a 2 hour computer workshop that demonstrates how the gene expression resources and tools available at the NCBI can be used to obtain qualitative and quantitative measurements of gene expression in different biological samples and under various experimental conditions

In this course, workshop participants will learn how to:

• Query the Gene Expression Omnibus (GEO) database and the two related Entrez databases, GEO Expressions and GEO DataSets to:
  • identify genes that may be regulated together and be part of a common regulatory pathway (profile neighbors);
  • use sequence similarity searching to find expression patterns for genes which may be members of a multi-gene family (sequence neighbors);
  • perform cross-species comparisons of expressed genes.
• Use the Digital Differential Display tool for the comparative analysis of mRNA abundance in cDNA (EST) libraries;
• Use the xProfiler tool to measure mRNA abundance in SAGE libraries;
• Mine the data in the Online Mendelian Inheritance in Man (OMIM) database and NCBI's variation database, dbSNP, to find polymorphisms that may alter gene expression;
• Integrate and visualize expression-related data (UniGene, SAGE tags, CpG islands and variation) in NCBI's genome browser, MapViewer.

Attendance at the lecture is a prerequisite for participation in the computer session.

For further information on Geo see: http://www.ncbi.nlm.nih.gov/geo/

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