EXPOLDB is a resource for investigating the natural variations in gene expression in humans and aims to provide insights into gene regulation by linking gene expression data from microarray experiments with the distribution of cis modulators of transcription. It is the first systematic effort to collect gene expression data from microarrays and link them with the distribution of (TG/CA)_n repeats. In this release version 1.0 , the database contains gene expression data of blood leukocytes from 13 normal human individuals (five pairs of monozygotic twins and 3 unrelated individuals) measured using HG U95Av2 oligonucleotide microarrays consisting probes for ~10,000 genes.

To make the results more comprehensive, information related to annotation, chromosomal location, cellular localization, Gene Ontology, biochemical roles of the gene products, biochemical pathways,tissue specific expression, and associated hyperlinks to other public databases have been provided.

Since the database incorporates both genotype and phenotype data from our own studies and other public databases, it can serve as a unique resource for the researchers investigating the effects of repetitive sequences on gene expression.

Tetrapodic layout of EXPOLDB

The mean expression for a gene represents the average level of expression of a gene as observed in blood leukocytes in array experiments. The metric CV is used to assess the variability in gene expression. The mean expression and CV of more than 5,000 genes can be accessed using this database.By specifying an appropriate CV range, genes that are highly variable,moderate or least variable can be identified in different datasets like unrelated individuals, twins and housekeeping genes or in a selected pathway.

The differentially expressed genes were identified by selecting those with 'present' (P) call and signal log ratio of more than 1.585 and using other standards as defined by Affymetrix (Sharma et al. 2005).

Housekeeping genesare defined as genes that are expressed constitutively in all tissues to maintain cellular functions. These genes are less likely to be affected by variations in tissue specific factors, number of different cell types in blood leukocytes and other structural alterations in chromatin structure that may vary between different individuals. The mean expression and variability of known human housekeeping genes across different individuals is provided
Least varying housekeeping genes
Highly expressed housekeeping genes

The expression and variation information for the above genes has been integrated with the description of intragenic and proximal (TG/CA)_n repeats in these genes. The information on the presence of known polymorphic repeats can also be obtained. It also provides information on the content of Alu repeats in these genes. The examples highlighting the implementation of EXPOLDB are presented below:
Housekeeping genes
Runt related transcription factor (RUNX) family
Eukaryotic Initiation Factor (EIF) housekeeping genes

SimRep identifies uninterrupted dinucleotide repeats and other simple repeats in a given nucleotide sequence. It reports the length and location of the specified repeat in the given sequence on both strands.

EXPOLDB can be used toexamine the expression and variability of genes involved in a biochemical pathway. For example, the query "Glycolysis" will retrieve the list of genes present in this pathway (based on KEGG and GenMAPP) depending on the the presence of the probe sets on the HG U95Av2 arrays or whether the genes had present (P) call in all the array experiments or the differential expression status.

(TG/CA)_n repeats as cis modulators of transcription
Examples of well studied genes regulated by (TG/CA)_n repeats are included for reference. The presence of (TG/CA)_n repeats have been shown to cause increase or decrease in expression in these genes.