ARpoNDB
Inference and comparison of bacterial 𝜎⁵⁴ sigmulon
Description
aRpoNDB is an accessible web platform for exploring and analyzing σ⁵⁴-dependent regulons across diverse bacterial phyla. Designed for ease of use, it provides researchers with organized, in-depth data on putative σ⁵⁴-regulated genes and DNA motifs within promoter sequences. Users can navigate through bacterial classes and genera, with each organism’s dedicated page showcasing predicted promoter genes, motif statistics, and detailed functional annotations. As a valuable resource for microbial genomics, aRpoNDB supports research in basic science, medicine, and agriculture, offering insights into the critical cellular roles of σ⁵⁴-regulated pathways.
Help / User Guide — Visualization of σ⁵⁴ regulons by organism
🎯 Main Objective
The central purpose is to present for each bacterial class, detailed information on a representative organism in which the σ⁵⁴-dependent regulon has been predicted. This prediction includes:
- Potential target genes regulated by σ⁵⁴ and their corresponding operon.
- The E-value from the hypergeometric distribution for the COG in which the target gene is classified. The gene’s functional description.
- The associated predicted promoter sequence, containing the σ⁵⁴ motif and the translation start site (ATG).
The main panel displays:
- Phylogenetic organization by class and genus.
- Presence/absence of σ⁵⁴ across the 33 studied bacterial classes, with color codes indicating their respective phyla.
- Pfam domain architecture of the σ⁵⁴ protein.
- Interactive visualizations of COG-based functional enrichment of σ⁵⁴ -regulated genes.
Specifically, the buttons corresponding to the 4 functional COG categories display enrichment graphs that illustrate:
Functional enrichment analysis of RNAP-σ⁵⁴-regulated genes in the 4 categories of COGs. These graphs illustrate the taxonomic distribution of genes regulated by the RNAP-σ⁵⁴ complex across functional subcategories within each category based on the COG hierarchy. Each data point is depicted as a circle, with the size of the circle indicating the negative log-transformed hypergeometric distribution value. This size variation provides a visual representation of the significance of the enrichment for the corresponding COG, thereby facilitating a more straightforward interpretation. To aid in differentiation, colors were assigned to each COG subcategory, as shown in each graph legend.
🔍 Navigation by class, genus, and organism
- In the left-hand panel, select a bacterial class (e.g., Bacteroidia, Aquificia, Thermodesulfobacteria).
- The analyzed genera within that class will appear.
- Upon selecting a genus, you will see the representative organism used in the analysis.
Example: In the class Sphingobacteriia, you can select the genus Anseongella and view the species Anseongella ginsenosidimutans.
📋 Main Panel: Genes regulated by σ⁵⁴
Once the organism is selected, a table is displayed with the following information per gene:
| Column | Description |
|---|---|
| Gene ID | Gene identifier in the genome |
| E-val | E-value of the hypergeometric distribution for the corresponding COG | Gene Description | Functional description of the gene |
| Promoter | Predicted regulatory sequence (σ⁵⁴ motif + ATG start region) |
| COG | Orthologous group code (if applicable) links to it's |
| COGs Classification | Functional category of the COG (e.g., metabolism, cell structure) |
| COG Description | Annotated function of the COG |
🧰 What can you do from here?
- Explore complete σ⁵⁴-dependent regulons across diverse bacterial classes and phyla.
- Compare the functional diversity of σ⁵⁴-regulated genes among microbial lineages.
- Download data: promoter sequences, gene lists, and functional annotations for downstream analyses.
The table may include genes predicted to be part of an operon. These genes are located downstream of the predicted promoter and may be under the same transcriptional regulation. The first gene in the operon (the one directly linked to the promoter) is highlighted in red.