> 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/icm/analyses/analysis-functionality/task-menu/ask-correlation-engine.md). # Ask Correlation Engine {% hint style="warning" %} AI-generated content may be inaccurate. {% endhint %} ## What is Ask Correlation Engine? It is a focused, read-only question-and-answer experience that helps interpret a finding from the analysis using evidence retrieved from Correlation Engine (CE). This is a research interpretation aid for research only use. ## Using Ask Correlation Engine * Click

at the bottom of the task graph in the Analyses tab

Click **Ask Correlation Engine** to select a highlighted completed result to ask about it, or ask a general question

Nodes that are available to be used will be colored. * Click an available node to select the node and choose to

Click a colored node to select the node then choose to **Ask a general question** or **Ask about a gene**

### Ask about a gene * Select a gene from the list (which contains genes found in the selected node) or type a gene in the text box to find then select {% hint style="warning" %} Genes in the list are ordered using the p-values in the selected analysis result, lowest first. {% endhint %}

Select a gene from the list or type a gene name to select

* Click **Continue** * Ask a question about this gene by entering it in the text box

Enter a question or select one of the Questions to try then click **Ask**

* Click **Ask** {% hint style="warning" %} Only the gene and organism are sent to Correlation Engine. Analysis results are not sent. {% endhint %} The CE results are reported.

The CE results are reported and can be further explored in CE using the **Explore in Correlation Engine** button

{% hint style="warning" %} The CE Body Atlas includes normal tissue expression data. No disease data is present in the Body Atlas. {% endhint %} ### Ask a General Question * Ask about a gene, SNP, tissue, or cell type.

Type a question in the text box or try one of the questions

The CE results are reported can be further explored in CE using the **Explore in Correlation Engine** button.

CE results are reported for the question asked

### Ask a question for the Atlas context If a CE Atlas node is selected, the

button can be selected.

**Ask a question for this context** (CE Atlas node)

* Enter a question * Click **Ask**

Enter a question for the biological signature derived from the selected atlas and click **Ask**

{% hint style="warning" %} Correlation Engine uses the selected biological signature as context for the question. The full analysis report is not searched, sent, or analyzed. {% endhint %} The CE results are reported and can be further explored in Correlation Engine.

The results are reported along with evidence, limitations, and suggested next questions

{% hint style="warning" %} Do not enter personal, patient, confidential, or proprietary information. AI-generated responses may be inaccurate; verify before use. {% endhint %} AI features can be turned off by an administrator in the [Admin console](https://help.connected.illumina.com/account-management/admin-console). [More information for Correlation Engine](https://support.illumina.com/sequencing/sequencing_software/basespace-correlation-engine/documentation.html) and [Correlation engine FAQs](https://accounts.public.ce.basespace.illumina.com/b/corp/faq.nb). --- # 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/icm/analyses/analysis-functionality/task-menu/ask-correlation-engine.md?ask=&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.