BMC Genomics (Oct 2006)

Expoldb: <ul>ex</ul>pression linked <ul>pol</ul>ymorphism <ul>d</ul>ata<ul>b</ul>ase with inbuilt tools for analysis of expression and simple repeats

  • Lancet Doron,
  • Strichman-Almashanu Liora,
  • Horn-Saban Shirley,
  • Mandapati Kiran,
  • Khandelwal Mamta,
  • Kumar Naveen,
  • Sharma Anu,
  • Sharma Vineet K,
  • Brahmachari Samir K,
  • Ramachandran Srinivasan

DOI
https://doi.org/10.1186/1471-2164-7-258
Journal volume & issue
Vol. 7, no. 1
p. 258

Abstract

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Abstract Background Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is associating genome wide transcription patterns with potential cis modifiers of gene expression. Description EXPOLDB, a novel Database, is a new effort addressing this need by providing information on gene expression levels variability across individuals, as well as the presence and features of potentially polymorphic (TG/CA)n repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)n repeats. One of the unique features of this database is the display of expression data for 5 pairs of monozygotic twins, which allows identification of genes whose variability in expression, are influenced by non-genetic factors including environment. In addition to queries by gene name, EXPOLDB allows for queries by a pathway name. Users can also upload their list of HGNC (HUGO (The Human Genome Organisation) Gene Nomenclature Committee) symbols for interrogating expression patterns. The online application 'SimRep' can be used to find simple repeats in a given nucleotide sequence. To help illustrate primary applications, case examples of Housekeeping genes and the RUNX gene family, as well as one example of glycolytic pathway genes are provided. Conclusion The uniqueness of EXPOLDB is in facilitating the association of genome wide transcription variations with the presence and type of polymorphic repeats while offering the feature for identifying genes whose expression variability are influenced by non genetic factors including environment. In addition, the database allows comprehensive querying including functional information on biochemical pathways of the human genes. EXPOLDB can be accessed at http://expoldb.igib.res.in/expol