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Title page for ETD etd-03292010-120411


Type of Document Master's Thesis
Author Jourquin, Jerome
Author's Email Address jerome.jourquin@vanderbilt.edu
URN etd-03292010-120411
Title Gene List Automatically Derived For You (GLAD4U): deriving and prioritizing gene lists from PubMed literature
Degree Master of Science
Department Biomedical Informatics
Advisory Committee
Advisor Name Title
Bing Zhang Committee Chair
Daniel R. Masys Committee Member
Hua Xu Committee Member
Keywords
  • disease candidate genes
  • prioritization evaluation
  • data integration
  • NCBI resources
Date of Defense 2010-03-22
Availability unrestricted
Abstract

Answering questions such as “Which genes are related to breast cancer?” usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and manually creating gene lists. This process is both time-consuming and prone to errors.

We report GLAD4U (Gene List Automatically Derived For You), a novel, free web-based gene retrieval and prioritization tool. The quality of gene lists created by GLAD4U for three Gene Ontology terms and three disease terms was assessed using “gold standard” lists curated in public databases. We also compared the performance of GLAD4U with that of another gene prioritization software, EBIMed.

GLAD4U has a high overall recall. Although precision is generally low, its prioritization methods successfully rank truly relevant genes at the top of generated lists to facilitate efficient browsing. GLAD4U is simple to use, and its interface can be found at: http://bioinfo.vanderbilt.edu/glad4u.

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