Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.
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.


METHODS
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.


CONCLUSIONS
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.
Sharma
Vineet K
VK
G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India. vineetks@gmail.com
Sharma
Anu
A
Kumar
Naveen
N
Khandelwal
Mamta
M
Mandapati
Kiran Kumar
KK
Horn-Saban
Shirley
S
Strichman-Almashanu
Liora
L
Lancet
Doron
D
Brahmachari
Samir K
SK
Ramachandran
Srinivasan
S
D020029:Base Pairing / Q000235:genetics; D030541:Databases, Genetic; D015870:Gene Expression; D015894:Genome, Human / Q000235:genetics; D006019:Glycolysis / Q000235:genetics; D006801:Humans; D020407:Internet; D011110:Polymorphism, Genetic / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface