> 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/pharmaco-atlas.md).

# Pharmaco Atlas

**Pharmaco Atlas** finds compounds and treatments statistically correlated with a gene, sequence region, biogroup, or bioset. Results are ranked in order of statistical significance, helping researchers connect molecular data to relevant drug and chemical exposure contexts.

## What Can You Query?

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

To find all studies related to a specific compound (rather than finding compounds related to a gene), use [Curated Studies](/correlation-engine/querying-and-interpreting-results/curated-studies.md) — Pharmaco Atlas does not accept compound names as query input.

## How to Query Pharmaco Atlas

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

1. Enter the term in the query field.
2. Click the **Pharmaco Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-caba3344a1eb17a5e0a7f5b15975cc35f3613112%2Fimage%20\(17\).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 **Pharmaco Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-caba3344a1eb17a5e0a7f5b15975cc35f3613112%2Fimage%20\(17\).png?alt=media).

## Understanding Pharmaco Atlas Results

Results are displayed on the **Correlated Compounds** tab as a ranked list of compounds and treatments correlated with your query term.

### Drilling into a Compound

Click a compound name to see a breakdown of supporting studies by organism and data type. Click **View Individual Studies** to see all studies correlated with your query term that are tagged with the specific compound.

Expand a study by clicking its name to reveal the biosets. Click a bioset name to see the per-gene statistics.

### The Studies For... Tab

Shows all public and private studies tagged with the compound that are significantly correlated with your query. The count may differ from the Correlated Compounds tab count for the same reasons as in Disease Atlas (multiple testing correction and private study exclusion from categorization).

### Compound Category Locator

When viewing by category, click a compound category name to jump to that group in the results. When viewing by rank, clicking a category name highlights all compounds in that group.

## Filtering (v2.8+)

Starting in v2.8.0, Pharmaco Atlas supports filtering of correlated compounds by **data type** and **organism**.

## Exporting Results

Click **Export Results** to download the correlated compounds list as a `.csv`.


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# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## 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/pharmaco-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.