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Delete Genes

Delete Genes

The Delete Genes feature allows you to simulate the effect of removing one or more genes from a metabolic model. Unlike Single-Gene Deletion (which iterates over each gene individually), this feature lets you delete a custom set of genes simultaneously, enabling multi-gene knockout studies and evaluation of combinatorial gene essentiality.

Workflow

Delete Genes

  1. Select the "Delete Genes" option under the Analysis Options dropdown.
  2. Choose the cellular objective function.
  3. Upload a CSV file containing the gene names to be deleted.
  4. Select the knockout mode — Temporary or Permanent.
  5. Review the results: objective function value, number of blocked reactions, and affected pathways.

Input

Cellular Objective

Select a cellular objective function (e.g., Biomass reaction) that the model will optimize after the gene deletion.

Gene List (CSV)

Upload a CSV file with a single column named Genes containing the gene identifiers to be deleted.

Format:

Genes
gene_1
gene_2
gene_3

Preparing the gene list

The gene list can be prepared in two ways:

  • Custom selection — manually curate genes of interest based on experimental evidence, literature, or hypothesis-driven analysis.
  • MetNetComp output — use gene deletion strategies provided by MetNetComp, a database that provides simulation-based gene deletion strategies for growth-coupled production in constraint-based metabolic networks. For designated target metabolites, MetNetComp computes maximal and minimal gene deletion strategies across multiple genome-scale models (e.g., E. coli, S. cerevisiae, M. tuberculosis). The gene deletion sets from MetNetComp can be directly used as input here to evaluate their effect on the model.

Knockout Modes

Temporary Gene Knockout

Deletes the selected genes from the model temporarily and displays the results — including the objective function value, the number of blocked reactions, and other affected metrics. Once you close the results dialog, the model reverts back to its original state. This is useful for exploratory analysis without permanently altering the model.

Permanent Gene Knockout

Deletes the selected genes from the model permanently. The gene–protein–reaction (GPR) associations are updated, and all reactions that become non-functional due to the deletion are removed. The model is irreversibly modified and subsequent analyses will operate on the reduced model.

Permanent changes

Permanent Gene Knockout modifies the model in place. Make sure to download a copy of the original model before applying permanent deletions.

How it Differs from Single-Gene Deletion

Feature Single-Gene Deletion Delete Genes
Scope Deletes one gene at a time, iterating over all genes Deletes a user-defined set of genes simultaneously
Purpose Identify individual gene essentiality Simulate multi-gene knockouts and combinatorial effects
Input No input required — runs automatically for each gene Requires a CSV file with target gene names
Persistence Results only — model is never modified Supports both temporary and permanent knockout modes
Use case Genome-wide essentiality screening Targeted knockout studies, pathogen-specific gene removal