> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/correlation-engine/querying-and-interpreting-results/knockdown-atlas.md).

# Knockdown Atlas

**Knockdown Atlas** finds genes whose genetic perturbation (knockdown, knockout, overexpression, or silencing) is correlated with your query term. It lets you perform a reverse genetic perturbation analysis — starting from a gene signature or individual gene and discovering which experimental perturbations produced a similar effect.

{% hint style="info" %}
The app is called "Knockdown Atlas" because knockdowns and knockouts are the predominant experiment type covered, but results also include overexpression and other genetic perturbation studies.
{% endhint %}

## What Can You Query?

Knockdown Atlas accepts: **genes, sequence regions, biogroups, and biosets**.

## How to Query Knockdown Atlas

**With a gene, region, or biogroup:**

1. Enter the term in the query field.
2. Click the **Knockdown Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-10cb142ffde68564d48a515db2f09b98f10a209b%2Fimage%20\(21\).png?alt=media) in the app menu.

**With a bioset:**

1. Find the bioset and click the **mini-QuickView icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-0a2038f7d8421f594197b4726f532faff61affd8%2Fimage.png?alt=media) next to its name.
2. Click the **Knockdown Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-10cb142ffde68564d48a515db2f09b98f10a209b%2Fimage%20\(21\).png?alt=media).

## Understanding Knockdown Atlas Results

Results are displayed on the **Perturbed Genes** tab — a ranked list of genes whose perturbation is correlated with your query term.

### Drilling into a Perturbed Gene

Click a gene name to see a breakdown of supporting studies by organism and data type. The directional arrow indicates the effect on your query term — an up arrow means the perturbation up-regulates the query, a down arrow means it down-regulates it.

Click **View Individual Studies** to see all studies in which the specific perturbation was found to significantly affect your query term. Expand a study to see its biosets; click a bioset to see the full gene-level statistics.

### Finding All Genes Affected by a Specific Perturbation

To find all genes affected by perturbing a specific gene (the reverse of the above), use Curated Studies:

1. Clear any current query and click the Curated Studies icon ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-e2ac8bab87e60ffe145a4d32146916b2fb8f69a4%2Fimage%20\(5\).png?alt=media).
2. Click **All Curated Studies**.
3. Filter by the keyword (perturbed gene name).
4. Click **Advanced** and check **Mutant vs. wildtype** in the Experiment Design menu.
5. Apply the filter.

### The Studies For... Tab

Shows all studies in which a genetic perturbation significantly affected your query term. The count may differ from the Perturbed Genes tab for the same reasons as in other atlas apps (multiple testing correction and private study categorization rules).

## Filtering (v2.8+)

Starting in v2.8.0, Knockdown Atlas supports filtering of perturbed genes by **data type** and **organism**. The number of results returned was also expanded in this version.

## Exporting Results

Click **Export Results** to download the perturbed genes list as a `.csv`.


---

# Agent Instructions
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## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/correlation-engine/querying-and-interpreting-results/knockdown-atlas.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.