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

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

<p>Abstract</p> <p>Background</p> <p>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 tran...

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Main Authors: Lancet Doron, Strichman-Almashanu Liora, Horn-Saban Shirley, Mandapati Kiran, Khandelwal Mamta, Kumar Naveen, Sharma Anu, Sharma Vineet K, Brahmachari Samir K, Ramachandran Srinivasan
Format: Article
Language:English
Published: BMC 2006-10-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/7/258
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spelling doaj-da3ed014ca394053b768440ee93f5a092020-11-25T00:27:21ZengBMCBMC Genomics1471-21642006-10-017125810.1186/1471-2164-7-258Expoldb: <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 repeatsLancet DoronStrichman-Almashanu LioraHorn-Saban ShirleyMandapati KiranKhandelwal MamtaKumar NaveenSharma AnuSharma Vineet KBrahmachari Samir KRamachandran Srinivasan<p>Abstract</p> <p>Background</p> <p>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 <it>cis </it>modifiers of gene expression.</p> <p>Description</p> <p>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)<sub>n </sub>repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)<sub>n </sub>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 <it>RUNX </it>gene family, as well as one example of glycolytic pathway genes are provided.</p> <p>Conclusion</p> <p>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.</p> <p>EXPOLDB can be accessed at <url>http://expoldb.igib.res.in/expol</url></p> http://www.biomedcentral.com/1471-2164/7/258
collection DOAJ
language English
format Article
sources DOAJ
author Lancet Doron
Strichman-Almashanu Liora
Horn-Saban Shirley
Mandapati Kiran
Khandelwal Mamta
Kumar Naveen
Sharma Anu
Sharma Vineet K
Brahmachari Samir K
Ramachandran Srinivasan
spellingShingle Lancet Doron
Strichman-Almashanu Liora
Horn-Saban Shirley
Mandapati Kiran
Khandelwal Mamta
Kumar Naveen
Sharma Anu
Sharma Vineet K
Brahmachari Samir K
Ramachandran Srinivasan
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
BMC Genomics
author_facet Lancet Doron
Strichman-Almashanu Liora
Horn-Saban Shirley
Mandapati Kiran
Khandelwal Mamta
Kumar Naveen
Sharma Anu
Sharma Vineet K
Brahmachari Samir K
Ramachandran Srinivasan
author_sort Lancet Doron
title 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
title_short 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_sort 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
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2006-10-01
description <p>Abstract</p> <p>Background</p> <p>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 <it>cis </it>modifiers of gene expression.</p> <p>Description</p> <p>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)<sub>n </sub>repeats. EXPOLDB thus enables associating transcription levels with the presence and length of (TG/CA)<sub>n </sub>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 <it>RUNX </it>gene family, as well as one example of glycolytic pathway genes are provided.</p> <p>Conclusion</p> <p>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.</p> <p>EXPOLDB can be accessed at <url>http://expoldb.igib.res.in/expol</url></p>
url http://www.biomedcentral.com/1471-2164/7/258
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