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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth183
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 28, 2003
Revised March 4, 2004
Accepted March 10, 2004

Applications note

A tool for gene expression based PubMed search through combining data sources

Maksym Korotkiy 1, Rutger Middelburg 2, Henk Dekker 2, Frank van Harmelen 1, Jan Lankelma 3*

1 Division of Computer Science, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
2 Department of Medical Oncology, VU Medical Center, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
3 Department of Medical Oncology, VU Medical Center, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands; Tumor Cell Biology Group, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands

* To whom correspondence should be addressed. E-mail: jan.lankelma{at}falw.vu.nl.


  Abstract

Summary: We present a new tool for the semiautomated querying of PubMed using a batch of tens to thousands of GenBank accession numbers or UniGene cluster ids. By combining information from UniGene and SWISS-PROT, microGENIE obtains information on the biological relevance of expressed genes, as identified by micro-array experiments, with minimal user intervention and time investment.

Availability: microGENIE is freely available from http://www.cs.vu.nl/microgenie

Supplementary information: the web site above supplies examples of input and output files.


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