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. 2020 Jan 1:2020:baz149.
doi: 10.1093/database/baz149.

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Basten L Snoek  1   2 , Mark G Sterken  1 , Margi Hartanto  1   3 , Albert-Jan van Zuilichem  1 , Jan E Kammenga  1 , Dick de Ridder  3 , Harm Nijveen  3
Affiliations

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Basten L Snoek et al. Database (Oxford). .

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. Database URL: www.bioinformatics.nl/WormQTL2/.

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Figures

Figure 1
Figure 1
WormQTL2 Homepage. On the top of the page, the navigation bar can be found. This includes the WormQTL2 logo, which functions as a home button. It also includes a fast link to the Correlation and Locus overviews as well as links for help, data download and visual examples. The search box is located in the center, in which genes, phenotypes and GO terms can be entered. Shown in the blue middle square are the buttons for the investigations of single traits, correlating QTL profiles, QTLs at a specific locus, all eQTLs of an experiment, eQTLs per GO term and a list of all phenotypes for which QTLs can be shown. On the right side, a bar with information about WormQTL2 and QTLs in general can be found.
Figure 2
Figure 2
eQTL profiles of gmd-2 from all experiments hosted in WormQTL2. The significance profile (−log10(p)) per experiment for gmd-2 is shown in different colors per experiment. The legend is shown on the right and shows the colors for the different experiments. Chromosomes are indicated by different gray backgrounds and below the x-axis. The web-based plot is interactive; a mouse over provides the exact base pair position of each QTL or other point on the profile.
Figure 3
Figure 3
Correlation between eQTL profiles of pgp-7, pgp-6 and pgp-5. Correlation between the eQTL profile of pgp-7 and the other genes was set to report those profiles with a Pearson correlation >0.9, see navigation bar at the top. Genes are shown in different colors. The legend is shown on the right. Chromosomes are indicated by different gray backgrounds and below the x-axis. The web-based plot is interactive; a mouse over provides the exact base pair position of each QTL or other point on the profile.
Figure 4
Figure 4
Co-locating eQTL profiles of genes annotated with GO term ‘regulation of cell cycle’. The eQTL profiles of the top-15 highest eQTLs are shown as profiles. A histogram of all peaks −log10(p) > 3.5 is shown below the profile plot to detect possible regulatory hotspots, as can be observed here on chromosome I. Genes are shown in different colors. The legend is shown on the right. Chromosomes are indicated by different gray backgrounds and below the x-axis. The web-based plot is interactive; a mouse over provides the exact base pair position of each QTL or other point on the profile.
Figure 5
Figure 5
eQTL transband on chromosome X in Rockman et al. (67). The eQTL profiles of the top-15 highest eQTLs at marker rmm1258 in Rockman et al. are shown as profiles. Colors indicate different genes. The legend is shown on the right. Chromosomes are indicated by different gray backgrounds and below the x-axis. The web-based plot is interactive; a mouse over provides the exact base pair position of each QTL or other point on the profile. Moreover, more than the top-15 can be added to the plot creating a custom overview.
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