> For the complete documentation index, see [llms.txt](https://help.correlationengine.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.correlationengine.illumina.com/readme.md).

# Correlation Engine User Guide

**Illumina Correlation Engine** is a cloud-based multidimensional integration platform designed for exploratory, preclinical, and early translational research in drug discovery and biotechnology. It enables researchers to search and correlate global collections of heterogeneous, large-scale experimental data across diverse platforms, organisms, and therapeutic areas.

{% hint style="info" %}
Correlation Engine is available as part of the **Illumina Connected Multiomics Professional** subscription. Users of the Basic tier can access a limited view of public content; full import, querying, and export capabilities require a Professional or Enterprise license.
{% endhint %}

## What Correlation Engine Does

Correlation Engine lets you place your experimental results within the context of the world's genomic experiments. Starting from a gene, concept, sequence region, or your own experimental dataset (a **bioset**), you can:

* **Discover disease associations** — find diseases, traits, and conditions statistically correlated with your data using Disease Atlas.
* **Identify tissue and cell-type expression patterns** — query Body Atlas across 27,000+ curated public studies and single-cell datasets.
* **Find drug and compound correlations** — uncover treatments and chemical perturbations linked to your gene or bioset with Pharmaco Atlas.
* **Map genetic perturbation effects** — explore knockdown, knockout, and overexpression experiments via Knockdown Atlas.
* **Perform pathway enrichment** — identify significantly enriched Gene Ontology, MSigDB, and InterPro biogroups.
* **Run meta-analysis** — derive consensus gene signatures across up to 150 biosets simultaneously.
* **Search literature and clinical trials** — access relevant PubMed publications and ClinicalTrials.gov entries alongside your data.

## How This Guide Is Organized

| Section                                                                                     | What You'll Learn                                      |
| ------------------------------------------------------------------------------------------- | ------------------------------------------------------ |
| [About](/about/about.md)                                                                    | Platform overview and demo videos                      |
| [Introduction](/introduction/introduction.md)                                               | How to access CE through Illumina Connected Multiomics |
| [Data Inputs](/data-inputs/data-inputs.md)                                                  | Getting data into CE from ICM or local upload          |
| [Managing My Data](/managing-my-data-in-correlation-engine/managing-data.md)                | Projects, studies, groups, and libraries               |
| [Querying and Interpreting Results](/querying-and-interpreting-results/querying-results.md) | App-by-app query guide                                 |
| [Reference](/reference/release-notes.md)                                                    | Release notes and FAQs                                 |

## Additional Resources

| Link                                                                          | Description                                 |
| ----------------------------------------------------------------------------- | ------------------------------------------- |
| [Illumina Connected Multiomics Help](https://help.connected.illumina.com/icm) | Full ICM user documentation                 |
| [Correlation Engine Help Site](https://help.correlationengine.illumina.com/)  | Original CE help site (release notes, FAQs) |
| <customercare@illumina.com>                                                   | Contact Illumina support                    |


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