How to Use devQTL
The main purpose of devQTL is to allow other researchers to utilize the platform developed in this study. Candidate genes may be searched through this website by specifying a particular genomic region of interest (i.e., QTL) within a particular chromosome by specifying the (a) boundary physical positions (bp), (b) status of genes to be included, (c) temporal parameters (developmental stages to determine TPM expression levels), and/or (d) spatial parameters (anatomical structures in the developing embryo for co-expression analysis). This initial set of candidate genes may be filtered based on coding non-synonymous single nucleotide polymorphisms (nsSNPs) between two intercross strains of interest.
Use the physical positions (bp) of two specific markers in Mus musculus from the primary reference assembly (GRCm38) to define the boundaries of your region of interest. To determine the position of each marker, go to either NCBI SNP or UniSTS. Type the name of the marker and click "Go" or hit "Enter." This will lead you to a page showing a short description of the marker. Click on the hyperlink for that specific marker to go the comprehensive marker page. For SNPs, go to the "Integrated Maps" portion and look under the column "Group Term" and choose the row that corresponds to "Primary Assembly" with MGSCv37 as its "Group Label." Within that row, look under the column "Chr Pos" to obtain the physical position of that particular SNP. For STS markers, go to the "Mapping Information" portion. Choose the Sequence Map that corresponds to the reference assembly (the one that only mentions the chromosome number and is not from Mm_Celera) and use the range indicated by the Position as your query.
To obtain your initial list of genes, choose the specific chromosome of interest then specify your region of interest using the physical positions of the markers above separated by 2 dots (e.g., 100000000..110000000). Specify the flanking distance (bp) that would be included upstream and downstream of the region of interest. Then choose whether you need predicted genes only, known genes only, or all of the genes. You may also select the specific temporal and/or spatial parameters. For the temporal parameters, you may choose from looking at expression levels: (a) within one stage, (b) from two separate stages where the final expression level will be based on the total transcripts per million (TPM) levels of the two chosen stages, and (c) within a range of stages where the final expression level will be based on all of TPMs of the stages included within the specified range. Then specify expression level cut-off between 0 to 100. Inclusion of the spatial parameters is still in progress. Finally, click "Get Genes" to obtain the results. Use the regular "Back" button of your browser to return to this page if you want to make another query. Click on "Start Over" before plugging in new values.
