Pathway-to-Model Reference Chart: Genes × Recommended Cell Models

Forty gene and pathway entries, each mapped to four things:

• • the question the gene is usually studied to answer,
• • the model that can answer it,
• • the readout that carries weight,
• • and the artefact most often mistaken for a result.

It exists because the most common model failure is not technical. It is choosing a cell system that cannot express the pathway in question, then interpreting the absence of a phenotype as biology. The chart makes that mismatch visible before the build.

The full chart is a two-sheet spreadsheet: the matrix itself, and a "how to use" page with the three rules that apply to every row.

Forty entries cover Hippo, WNT, PI3K–AKT, immune checkpoints and targets, hepatic and β-cell metabolism, fatty-acid oxidation and glycolysis, common cancer dependencies, and the neurodegeneration genes most often modelled in iPSC-derived cells.

A model that lacks the pathway cannot report on it. Check baseline pathway activity in the model before editing anything. A knockout in a line where the pathway is already off will look inert, and that is a statement about the line.

One readout is never enough. Pair a pathway-state readout (localization, phospho-signal, reporter) with a functional endpoint (growth, secretion, killing). The first explains the mechanism; the second shows it matters.

Context is part of the claim. Lineage, passage, stimulation and media all change pathway state. A row in this chart tells you what to measure, not what you will find.

Send us the gene or pathway node and the cell type you have access to. We will tell you whether the model can support the question, which readout to build first, and what the pilot should look like — before a single guide is ordered.

Contact EDITGENE to request a project consultation or quote.

Entries reflect common practice across published work; model performance varies by protocol, passage, and donor. The chart is a planning aid, not a protocol library.

Every recommendation should be confirmed with a pilot in the intended cell type before a build is committed.

• • Tsherniak A, et al. Defining a cancer dependency map. Cell. 2017;170:564–576.
• • Nott A, et al. Brain cell type-specific enhancer–promoter interactome maps and disease-risk association. Science. 2019;366:1134–1139.
• • Fruman DA, et al. The PI3K pathway in human disease. Cell. 2017;170:605–635.