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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...
Autores principales: | , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618849/ https://www.ncbi.nlm.nih.gov/pubmed/17038195 http://dx.doi.org/10.1186/1471-2164-7-258 |
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author | Sharma, Vineet K Sharma, Anu Kumar, Naveen Khandelwal, Mamta Mandapati, Kiran Kumar Horn-Saban, Shirley Strichman-Almashanu, Liora Lancet, Doron Brahmachari, Samir K Ramachandran, Srinivasan |
author_facet | Sharma, Vineet K Sharma, Anu Kumar, Naveen Khandelwal, Mamta Mandapati, Kiran Kumar Horn-Saban, Shirley Strichman-Almashanu, Liora Lancet, Doron Brahmachari, Samir K Ramachandran, Srinivasan |
author_sort | Sharma, Vineet K |
collection | PubMed |
description | 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 |
format | Text |
id | pubmed-1618849 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-16188492006-10-21 Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats Sharma, Vineet K Sharma, Anu Kumar, Naveen Khandelwal, Mamta Mandapati, Kiran Kumar Horn-Saban, Shirley Strichman-Almashanu, Liora Lancet, Doron Brahmachari, Samir K Ramachandran, Srinivasan BMC Genomics Database 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 BioMed Central 2006-10-13 /pmc/articles/PMC1618849/ /pubmed/17038195 http://dx.doi.org/10.1186/1471-2164-7-258 Text en Copyright © 2006 Sharma et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Sharma, Vineet K Sharma, Anu Kumar, Naveen Khandelwal, Mamta Mandapati, Kiran Kumar Horn-Saban, Shirley Strichman-Almashanu, Liora Lancet, Doron Brahmachari, Samir K Ramachandran, Srinivasan Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title | Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title_full | Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title_fullStr | Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title_full_unstemmed | Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title_short | Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
title_sort | expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618849/ https://www.ncbi.nlm.nih.gov/pubmed/17038195 http://dx.doi.org/10.1186/1471-2164-7-258 |
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