In the overview page, you will find expression information of detected BGCs based on your RNA-seq experiments. Overview can be sorted by the selected column title e.g. "Average fold change..."

1. "Region" column denotes the region numbers given by antiSMASH.
2. "BGC name" column denotes a similar (if similarity is detected by antiSMASH) BGC defined in MiBIG.
3. Third column is the overview of genes residing in the BGC, pretty self-explanatory.
4. Average fold change column simply shows a summary of the fold change (calculated from core biosynthetic genes) between conditions for each experiment for the respective BGC.
5. Final column is a simple representation of the BGCs expression level, compared to specific references:
   1. "Housekeeping genes": Mean value of expression levels (TPMs) of all the housekeeping genes detected in the genome
   2. "Non housekeeping genes": Mean value of expression levels (TPMs) of all the non housekeeping genes detected in the genome
   3. "Mean expression": Mean value of expression levels (TPMs) of all the genes in the genome.

If the button left of the "Region" column is clicked, there will be an overview of a single BGC in terms of the expressions and fold changes of all the genes inside the cluster, per experiment. Genes marked inside black boxes are the "core biosynthetic" genes defined by antiSMASH.

Once the "ANALYZE IN DETAIL" button is clicked for a BGC in the overview page, you will be directed to BGC specific results. At the top part, the settings for visualization can be found. In detail, you can view "Fold changes" or "Normalized expression" (TPM) values in selected experiments and search for specific KEGG terms throughout the genome or cluster. "Secondary Metabolism Specific" KEGG terms describes genes which are also annotated in "biosynthesis of secondary metabolites" or "biosynthesis of antibiotics" pathways ("ko01130", "ko01110").

Second part of detailed BGC analysis involves the visualization of the expression/fold-change of selected BGC and selected genes from KEGG or other sources in the page. Here you can search by genes and their neighbouring genes by "gene id" or clicking specific genes from the tables shown in the bottom part of the page.

Finally, you can explore the genes that have co-regulated the most with your BGC of interest based on your experiments. At the top part you can select functional annotation of the genes that are mostly responsible for BGC expression such as "Transport", "Regulation", "Resistance genes". Since we have selected (seen two images above) to view the "drug exporter" genes, such functionally annotated genes are highlighted. Concordant regulation means that the gene and the BGC have the same expression change direction e.g. both are over-expressed/under-expressed. Discordant denotes that the expression changes are reversely correlated e.g. a specific repressor is under-expressed and the BGC is over-expressed. The "SCO6666" gene is shown to be regulating "actinorhodin" expression by Lee, N., Kim, W., Chung, J. et al. Please note that a high score doesn’t necessarily prove an association between a BGC and a gene. It rather points to high expression changes in the different conditions relative to a BGC of interest.