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An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases

BACKGROUND: Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, mos...

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Autores principales: Yang, Jin Ok, Hwang, Sohyun, Oh, Jeongsu, Bhak, Jong, Sohn, Tae-Kwon
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638159/
https://www.ncbi.nlm.nih.gov/pubmed/19091018
http://dx.doi.org/10.1186/1471-2105-9-S12-S19
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author Yang, Jin Ok
Hwang, Sohyun
Oh, Jeongsu
Bhak, Jong
Sohn, Tae-Kwon
author_facet Yang, Jin Ok
Hwang, Sohyun
Oh, Jeongsu
Bhak, Jong
Sohn, Tae-Kwon
author_sort Yang, Jin Ok
collection PubMed
description BACKGROUND: Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. RESULTS: To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page , and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. CONCLUSION: Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.
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spelling pubmed-26381592009-02-11 An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases Yang, Jin Ok Hwang, Sohyun Oh, Jeongsu Bhak, Jong Sohn, Tae-Kwon BMC Bioinformatics Research BACKGROUND: Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. RESULTS: To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page , and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. CONCLUSION: Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals. BioMed Central 2008-12-12 /pmc/articles/PMC2638159/ /pubmed/19091018 http://dx.doi.org/10.1186/1471-2105-9-S12-S19 Text en Copyright © 2008 Yang 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 Research
Yang, Jin Ok
Hwang, Sohyun
Oh, Jeongsu
Bhak, Jong
Sohn, Tae-Kwon
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title_full An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title_fullStr An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title_full_unstemmed An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title_short An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
title_sort integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638159/
https://www.ncbi.nlm.nih.gov/pubmed/19091018
http://dx.doi.org/10.1186/1471-2105-9-S12-S19
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