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. 2006 Oct 13:7:258.
doi: 10.1186/1471-2164-7-258.

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

Vineet K Sharma  1 , Anu Sharma, Naveen Kumar, Mamta Khandelwal, Kiran Kumar Mandapati, Shirley Horn-Saban, Liora Strichman-Almashanu, Doron Lancet, Samir K Brahmachari, Srinivasan Ramachandran
Affiliations

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

Vineet K Sharma et al. BMC Genomics. .

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.

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Figures

Figure 1
Figure 1
Tetrapodic layout of EXPOLDB: The 4 domains of layout are shown in bold face type. Note that all attributes of a gene are singularly linked to its official HGNC symbol serving as the primary key
Figure 2
Figure 2
A summary of the expression patterns and repeat distribution in genes of the glycolytic pathway.
See this image and copyright information in PMC

References

    1. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2006:D173–D180. doi: 10.1093/nar/gkj158. - DOI - PMC - PubMed
    1. Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright IJ, Smith CM, Beal JS, Corbani LE, Blake JA, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res. 2004:D568–D571. doi: 10.1093/nar/gkh069. - DOI - PMC - PubMed
    1. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA. 2002;99:4465–4470. doi: 10.1073/pnas.012025199. - DOI - PMC - PubMed
    1. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996;380:152–154. doi: 10.1038/380152a0. - DOI - PubMed
    1. Brahmachari SK, Meera G, Sarkar PS, Balagurumoorthy P, Tripathi J, Raghavan S, Shaligram U, Pataskar S. Simple repetitive sequences in the genome: structure and functional significance. Electrophoresis. 1995;16:1705–1714. doi: 10.1002/elps.11501601283. - DOI - PubMed

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