WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Basten L. Snoek, Mark G. Sterken, Margi Hartanto, Albert-Jan Van Zuilichem, Jan E. Kammenga, Dick De Ridder, Harm Nijveen

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

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.
Original languageEnglish
Article numberbaz149
JournalDatabase : the Journal of Biological Databases and Curation
Volume2020
DOIs
Publication statusPublished - 21 Jan 2020

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Quantitative Trait Loci
Caenorhabditis elegans
Gene expression
quantitative trait loci
Genes
Gene Expression
Gene-Environment Interaction
Data Mining
Publications
Meta-Analysis
Experiments
Databases
Genetics
gene expression
loci
quantitative genetics
linkage (genetics)
Nematoda

Cite this

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title = "WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans",
abstract = "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.",
author = "Snoek, {Basten L.} and Sterken, {Mark G.} and Margi Hartanto and {Van Zuilichem}, Albert-Jan and Kammenga, {Jan E.} and {De Ridder}, Dick and Harm Nijveen",
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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.

In: Database : the Journal of Biological Databases and Curation, Vol. 2020, baz149, 21.01.2020.

Research output: Contribution to journalArticleAcademicpeer-review

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