> 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/disease-atlas.md). # Disease Atlas **Disease Atlas** is a CE app that finds diseases, traits, conditions, and surrogate endpoints statistically correlated with a gene, SNP, sequence region, biogroup, or bioset. Results are grouped by disease category and ranked by statistical significance. {% hint style="info" %} Disease Atlas categories include only phenotypes specifically tagged as "disease." Broader phenotypes like "aging" are not listed as Disease Atlas categories but can be found via Curated Studies. {% endhint %} ## What Can You Query? Disease Atlas accepts: **genes, SNPs, sequence regions, biogroups, and biosets**. To find all studies related to a disease (rather than finding diseases related to a gene), use [Curated Studies](/correlation-engine/querying-and-interpreting-results/curated-studies.md) — Disease Atlas does not accept disease names as query input. ## How to Query Disease Atlas **With a gene, SNP, region, or biogroup:** 1. Enter the term in the query field. 2. Click the **Disease Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-21f9ef54538c9550f426bc292d9b7b780f49e673%2Fimage%20\(13\).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 **Disease Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-21f9ef54538c9550f426bc292d9b7b780f49e673%2Fimage%20\(13\).png?alt=media). ## Understanding Disease Atlas Results Results are displayed on the **Correlated Diseases** tab. Diseases are grouped into broad disease categories (e.g., Oncology, Metabolic, Neurological). **View options:** * **By category** (default) — grouped into disease categories; click a disease category name to jump to it. * **By rank** — sorted by statistical score; clicking a category name highlights all diseases belonging to it. ### Drilling into a Disease Click a disease name to see a breakdown of supporting studies by organism and data type. Then click **View Individual Studies** to see all studies with a significant correlation to your query term that are tagged with that disease. Expand a study by clicking its name to reveal the contributing biosets. Click a bioset name to see the statistics (fold change, p-value, copy number change, etc.) for that bioset. ### The Studies For... Tab The **Studies For...** tab shows all public and private studies tagged with the disease that are significantly correlated with your query. This count may differ from the Correlated Diseases count because: * The Correlated Diseases view groups results and applies additional statistical thresholds (e.g., multiple hypothesis testing correction) — some studies passing the simple study-level threshold may not appear at the categorized level. * Private studies appear in **Studies For...** but are not included in categorization (unless you are an Enterprise user with domain library studies). ## Scoring and Ranking CE's disease ranking considers: 1. The total number of disease-specific studies in which the query term was measured 2. The number of disease-specific studies in which the query term was found to be significant 3. The ranks of the query term in each disease study 4. The consistency of association across disease studies The top result is assigned a normalised score of 100; all other results are scaled relative to it. For detailed methodology, see [Kupershmidt et al., 2010, *PLoS ONE*](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013066). ## Filtering (v2.8+) Starting in v2.8.0, Disease Atlas supports filtering of correlated diseases by **data type** and **organism**, allowing you to restrict results to, for example, only human RNA expression studies. ## Exporting Results Click **Export Results** to download the full list of correlated diseases as a `.csv`. --- # 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/disease-atlas.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.