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Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.
Vineet K Sharma1, Anu Sharma, Naveen Kumar
1G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India. vineetks@gmail.com
BMC Genomics
|October 14, 2006
Summary
EXPOLDB is a new database linking human gene expression variability to polymorphic repeat variations and environmental influences. It helps researchers understand the genetic and non-genetic factors affecting gene expression. Keywords: gene expression, variability, polymorphic repeats, environmental factors, EXPOLDB.
Area of Science:
- Genomics
- Bioinformatics
- Human Genetics
Background:
- Quantitative variation in gene expression is linked to phenotypic differences in humans.
- Understanding gene expression variability requires associating transcription patterns with cis-acting genetic modifiers.
- Polymorphic repeats, such as (TG/CA)n, are potential modifiers of gene expression.
Purpose of the Study:
- To introduce EXPOLDB, a novel database for exploring gene expression variability.
- To enable association of genome-wide transcription patterns with polymorphic repeat presence and length.
- To facilitate the identification of genes influenced by non-genetic factors through twin expression data.
Main Methods:
- EXPOLDB integrates gene expression data with information on polymorphic (TG/CA)n repeats.
- The database supports queries by gene name, pathway name, and user-uploaded HGNC symbols.
- An online tool, SimRep, is available for identifying simple repeats in nucleotide sequences.
- Case examples, including housekeeping genes, the RUNX gene family, and glycolytic pathway genes, illustrate database applications.
Main Results:
- EXPOLDB provides a platform for associating gene expression levels with polymorphic repeat characteristics.
- The database includes expression data from monozygotic twin pairs to discern environmental influences on gene expression.
- Comprehensive querying capabilities allow exploration of gene expression within the context of biochemical pathways.
Conclusions:
- EXPOLDB uniquely facilitates the association of transcription variations with polymorphic repeats and environmental factors.
- The database aids in understanding the genetic and non-genetic basis of human gene expression variability.
- EXPOLDB offers a valuable resource for researchers investigating gene expression and its modifiers.
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