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The most relevant signaling or metabolic pathways and networks were identified using the "pathway to gene" option.
Identification of putative novel genes was performed using AUGUSTUS [ 49] with complete gene option enabled.
Clicking on the 'Syntenic gene' option opens the search syntenic genes page where checkboxes for 11 Brassicaceae species (B. napus contains the Brassica A and C subgenomes) allow users to choose their required searches; a syntenic gene search between A. thaliana and B. rapa is set as the default.
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If the user selects a particular gene, options to link out to the above mentioned biological databases become available.
Any sites with multiple transcripts resulting in multiple annotations were annotated only once using the by-gene option in VEP [ 35].
With the "Genes" option, ~11,000 genes were considered for the FDR-FET analysis.
These miR were predicted by miRNA viewer to target 47 "common genes" and 864 genes when the "all genes" option was chosen.
All this information can also be retrieved collectively for multiple genes by using the 'Advanced Query for Retrieving Data for Multiple Genes' option available on the Results page.
Since some dispensable genes are known lethal genes, an option, whether variants in dispensable genes are filtered out or not, is provided.
In the gene model option ASEQ matches coding SNPs and gene coordinates, whereas in the transcript model option transcript specific exon coordinates are considered for each SNP.
These are prime miR candidates that could be considered as a gene therapy option for patients suffering from chronic wounds.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com