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WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans
Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6971878/ https://www.ncbi.nlm.nih.gov/pubmed/31960906 http://dx.doi.org/10.1093/database/baz149 |
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author | Snoek, Basten L Sterken, Mark G Hartanto, Margi van Zuilichem, Albert-Jan Kammenga, Jan E de Ridder, Dick Nijveen, Harm |
author_facet | Snoek, Basten L Sterken, Mark G Hartanto, Margi van Zuilichem, Albert-Jan Kammenga, Jan E de Ridder, Dick Nijveen, Harm |
author_sort | Snoek, Basten L |
collection | PubMed |
description | Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/ |
format | Online Article Text |
id | pubmed-6971878 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-69718782020-01-24 WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans Snoek, Basten L Sterken, Mark G Hartanto, Margi van Zuilichem, Albert-Jan Kammenga, Jan E de Ridder, Dick Nijveen, Harm Database (Oxford) Original Article Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/ Oxford University Press 2020-01-21 /pmc/articles/PMC6971878/ /pubmed/31960906 http://dx.doi.org/10.1093/database/baz149 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Snoek, Basten L Sterken, Mark G Hartanto, Margi van Zuilichem, Albert-Jan Kammenga, Jan E de Ridder, Dick Nijveen, Harm WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title | WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title_full | WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title_fullStr | WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title_full_unstemmed | WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title_short | WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans |
title_sort | wormqtl2: an interactive platform for systems genetics in caenorhabditis elegans |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6971878/ https://www.ncbi.nlm.nih.gov/pubmed/31960906 http://dx.doi.org/10.1093/database/baz149 |
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