> 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/body-atlas.md). # Body Atlas **Body Atlas** is a unique CE app that maps gene expression across tissues, cell types, cell lines, stem cells, and single-cell populations. It functions as a comprehensive expression atlas built from thousands of normalised reference datasets. ## What Can You Query? | Query Input | Results | | ----------------------------------- | ------------------------------------------------------------ | | **Gene** | Tissues and cell types ranked by expression or correlation | | **Biogroup** | Tissues and cell types ranked by biogroup enrichment p-value | | **Bioset** | Tissues and cell types ranked by correlation score | | **Tissue or cell line (biosource)** | Genes ranked by expression level in that biosource | ## How to Query Body Atlas **With a gene, biogroup, or keyword:** 1. Enter your term in the query field. 2. Click the **Body Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-a46ccc48b6eca848285bc99f8dcb7d130db3ac49%2Fimage%20\(8\).png?alt=media) in the app menu. **With a bioset:** 1. Find a 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 **Body Atlas icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-a46ccc48b6eca848285bc99f8dcb7d130db3ac49%2Fimage%20\(8\).png?alt=media). ## Understanding Body Atlas Results ### Gene, Biogroup, or Bioset Query Results are grouped by **body system** by default (e.g., Nervous System, Cardiovascular, Digestive). Each result row represents a tissue, cell type, cell line, or stem cell population. Tabs allow you to switch between: * **Tissues** — normalised expression across anatomical tissues * **Cell Types** — expression in specific cell populations * **Cell Lines** — cancer and immortalised cell lines (also includes copy number and somatic mutation data) * **Stem Cells** — expression in stem cell populations * **Single Cell** — individual cell type signatures from scRNA-seq studies (added in v2.8+) **View options:** * **By category** — grouped into body systems; click a body system name to jump to that group * **By rank** — sorted purely by correlation score; clicking a body system name highlights all belonging tissues For **biogroup** queries, each result includes a **direction arrow** (up/down) indicating whether the overlapping genes are predominantly up- or down-regulated. For **bioset** queries, each result shows a **positive or negative correlation** indicator. ### Biosource (Tissue or Cell Line) Query When you query with a tissue or cell line name, Body Atlas returns a ranked list of genes expressed in that biosource. The **Tissue-Specific** tab shows genes with particularly high expression relative to other tissues. For cell lines, additional tabs show: * **Copy Number** — somatic copy number alterations * **Somatic Mutations** — mutation profiles ## Data Sources Body Atlas reference expression data is drawn from two main sources: **Microarray (default)** Drawn from Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array (human) and Affymetrix GeneChip® Mouse Genome 430A 2.0 Arrays (mouse). CE applies per-chip median normalisation and quantile normalisation across platforms. Coverage: * 128 human tissues from 1,068 arrays * 170 human cell types from 1,125 arrays * 748 human cell lines from 881 arrays * 52 stem cell types from 141 arrays * 151 mouse tissues from 2,730 arrays * 409 mouse cell types from 1,585 arrays **GTEx RNA-seq** Drawn from the Genotype-Tissue Expression (GTEx) project, processed through the RNA-Express pipeline. Coverage: 50 human tissues from 505 high-confidence RNA-seq samples. **Single-Cell (added in v2.5+ / expanded in v2.8+)** Single-cell RNA-seq biosets from CZI CELLxGENE and GEO, processed using Seurat. As of v2.9.0, 3,287 single-cell biosets are incorporated. Single-cell biosets are also available for direct inspection in Curated Studies. ## Venn Diagrams in Expanded Results When you expand a result row, a Venn diagram shows: * The number of genes in your queried biogroup or bioset * The number of genes in the correlated tissue/cell-type bioset * The number of genes in both The p-value represents the probability of that overlap occurring by chance if there were no biological link. ## Exporting Body Atlas Results Click the **Export** button on the right side of the results page to download a `.csv` of all results. --- # 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/body-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.