Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

[Preprint]. 2023 May 12:2023.05.11.540390. [Version 1] doi: 10.1101/2023.05.11.540390

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.

PMC Copyright notice

Figure 2. — A. A genome scan for Rab3b expression in the Diversity Outbred (J:DO) mice striatum identifies a strong (LOD > 65) cis-eQTL on chromosome 4. B. The allele effect plot for the haplotypes of the J:DO that regulate the expression of Rab3b. There are strong effects of WSB/EiJ, NZO/HILtJ, and C57BL/6J on the expression in one direction and 129S1/SvJ, CAST/EiJ, and A/J in the opposite direction. C. SNP association mapping within the QTL peak interval displaying all the SNPs that drive the QTL. Most of the highest score SNPs are around Rab3b, as expected for a gene regulated in cis. D. The genes that are negatively (Scp2-ps2) or positively (Ttc4, 0610037L13Rik, Zyg11b) correlated with Rab3b expression can be displayed. A scatter plot can be generated for each gene with the gene of interest. E. Mediation analysis can be performed on the data set to identify candidate causal mediators. This analysis retests the QTL effect at the locus of interest, iteratively conditioned on candidate mediators. Here the SNP in Scp2-ps2 creates the greatest LOD drop.

Figure 2. — A. A genome scan for Rab3b expression in the Diversity Outbred (J:DO) mice striatum identifies a strong (LOD > 65) cis-eQTL on chromosome 4. B. The allele effect plot for the haplotypes of the J:DO that regulate the expression of Rab3b. There are strong effects of WSB/EiJ, NZO/HILtJ, and C57BL/6J on the expression in one direction and 129S1/SvJ, CAST/EiJ, and A/J in the opposite direction. C. SNP association mapping within the QTL peak interval displaying all the SNPs that drive the QTL. Most of the highest score SNPs are around Rab3b, as expected for a gene regulated in cis. D. The genes that are negatively (Scp2-ps2) or positively (Ttc4, 0610037L13Rik, Zyg11b) correlated with Rab3b expression can be displayed. A scatter plot can be generated for each gene with the gene of interest. E. Mediation analysis can be performed on the data set to identify candidate causal mediators. This analysis retests the QTL effect at the locus of interest, iteratively conditioned on candidate mediators. Here the SNP in Scp2-ps2 creates the greatest LOD drop.