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If the user selects a particular gene, options to link out to the above mentioned biological databases become available.
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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.
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.
Any sites with multiple transcripts resulting in multiple annotations were annotated only once using the by-gene option in VEP [ 35].
Thus, to avoid as much as possible loss of putative target genes, relaxed options were used in miRGator [target genes predicted by at least one of the following programs: TargetScanS, miRanda and PicTar (4-way)].
If you know the TF's EntrezGene ID, select the "NCBI GeneID" option and enter it in the search field; otherwise, select the "Gene Symbol" option and enter the complete or partial TF's official gene or alias symbol.
Because the genes are typically encoded on large plasmids that contain additional antimicrobial resistance genes, therapeutic options are limited (3 ).
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