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GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP.

L Qin1, P Prins, J T Jones

  • 1The Graduate School for Experimental Plant Sciences, Laboratory of Nematology, Wageningen University and Research Center, Binnenhaven 10, 6709 PD Wageningen, The Netherlands. ling.qin@nema.dpw.wau.nl

Nucleic Acids Research
|March 27, 2001
PubMed
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This study introduces GenEST, a program linking DNA sequence databases with gene expression profiles. It efficiently identifies genes with specific expression patterns, aiding in the discovery of novel factors.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Large-scale genome and expressed sequence tag (EST) projects generate vast DNA sequence data.
  • Efficient methods are needed to link sequence databases with temporal and spatial gene expression profiles.

Purpose of the Study:

  • To demonstrate a powerful method for linking cDNA sequence data with transcript profiles using cDNA-AFLP.
  • To develop a computational tool (GenEST) for this linkage.

Main Methods:

  • Utilized cDNA-AFLP, a reproducible differential display technique.
  • Developed GenEST software to predict transcript-derived fragment (TDF) sizes from in silico-digested cDNA sequences.
  • Validated TDF predictions by sequencing bands from cDNA-AFLP gels.

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Main Results:

  • Successfully linked vast numbers of virtual TDFs to experimental TDFs from cDNA-AFLP gels.
  • Demonstrated efficient screening of cDNA sequence databases for genes with relevant expression profiles.
  • Identified novel pathogenicity factors in Globodera rostochiensis by combining ESTs and expression profiles.

Conclusions:

  • cDNA sequence databases can be efficiently screened to identify genes with specific expression profiles.
  • cDNA-AFLP data can be readily linked back to database sequences for gene identification.
  • This integrated approach facilitates the discovery of novel genes and functions, as exemplified in Globodera rostochiensis.