Gene ranking explorer

Mycobacterium tuberculosis Gene Viewer

Explore gene rankings by condition, compare profile patterns across conditions, and export clean figures for presentation or publication.

Condition -
Genes in dataset -
Rows shown -
Best visible rank -
About this Tool

This interactive Mycobacterium tuberculosis Gene Viewer helps users explore ranked gene-expression datasets across multiple experimental and clinical conditions. The tool displays a condition-specific ranking table, a cross-condition gene profile matrix, and summary views that highlight broadly conserved high- or low-ranking patterns. Users can select a condition of interest, search for individual genes, adjust the number of rows shown, filter the profile matrix by pattern, and choose which conditions to display. The platform is designed to support comparison of candidate antigens across environments and the preparation of presentation-ready outputs, including CSV and figure-style image exports.

A rank of 1 represents the highest-ranked gene within a given dataset or condition.

The values shown in this viewer are within-dataset gene ranks derived from sorted expression measurements, not raw expression values. Genes with identical or very similar expression may still appear in different positions because the source ranking requires a unique order. Small differences between adjacent ranks should therefore be interpreted cautiously; the tool is best used to identify broader expression patterns and higher- versus lower-ranked genes across conditions.

How to Use and Glossary

How to use

  1. Select a condition from the dropdown menu to view the ranked genes for that specific dataset.
  2. Use the search box to enter one or more Rv gene identifiers if you want to focus on particular targets.
  3. Adjust the Rows setting to control how many genes are displayed in the ranking table and gene profile matrix.
  4. Review the Ranking Table to see the order of genes in the selected condition, with the intensity bar showing relative rank position across the dataset.
  5. Use the Matrix conditions checkboxes to choose which experimental or clinical conditions should be shown in the Gene Profile Matrix.
  6. Use the Pattern view filter to switch between all genes, genes with broadly conserved high ranking across conditions, or genes with broadly conserved low ranking.
  7. Inspect the Gene Profile Matrix to compare how the same genes rank across multiple selected conditions.
  8. Open the Per Condition Ranking Summary section to view the top-ranked and low-ranked genes for each condition in a compact format.
  9. Export the current view using Export CSV, Export Dashboard JPEG, or Export Gene Matrix Figure if you want to save the analysis or prepare figures for reports and presentations.

Data sources

Gene rankings were normalised using data derived from the following published transcriptomic reference datasets:

  • Coppola M, Lai RP-J, Wilkinson RJ, Ottenhoff THM. The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung. Frontiers in Immunology. 2021;12:763364.
  • Bei C, Zhu J, Culviner PH, Gan M, Rubin EJ, Fortune SM, Gao Q, Liu Q. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. Nature Communications. 2024;15:3088.

Condition glossary

Condition labels shown in the viewer use the display names BMDM and THP-1 cells for the macrophage and THP-1 compendium datasets.

Comma, space, or semicolon separated

Ranking Table

Rank Gene
Rank intensity

Gene Profile Matrix

Values shown are normalised gene ranks from each study, where 1 represents the highest-ranked gene in that condition.

Per Condition Ranking Summary

Top 10 genes and low 10 genes from raw rankings in each condition.