> 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/biogroups.md). # Biogroups **Biogroups** (also called Pathway Enrichment) shows which canonical gene sets — from Gene Ontology, MSigDB, InterPro, and TargetScan — are significantly enriched in your queried bioset or are highly associated with a phenotype or compound. ## What Is a Biogroup? A **biogroup** is a named collection of genes associated with a specific biological function, pathway, protein family, or regulatory motif. Biogroups carry no numerical values — they are gene lists. CE tests whether the genes in a bioset significantly overlap with each biogroup using rank-based enrichment statistics. Biogroups in CE come from: | Source | Category | | ------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | | [Gene Ontology](http://www.geneontology.org/) | Biological processes, cellular components, molecular functions | | [MSigDB](http://www.broadinstitute.org/gsea/msigdb/index.jsp) | Canonical pathways, hallmark gene sets, positional sets, regulatory motifs, oncogenic signatures, immunologic signatures | | [InterPro](http://www.ebi.ac.uk/interpro/) | Protein families | | [TargetScan](http://www.targetscan.org/) | Predicted miRNA targets | ## What Can You Query? | Query Input | What You Get | | ------------------------- | ----------------------------------------------------------------------------- | | **Bioset** | Ranked list of biogroups that highly overlap with the bioset | | **Phenotype or compound** | Ranked list of biogroups that overlap with biosets tagged with the query term | {% hint style="info" %} Biogroups does not accept a gene or biogroup as a query input. To find which biogroups a gene belongs to, query QuickView and click the **General Info** tab. {% endhint %} ## How to Query Biogroups **With a phenotype or compound:** 1. Enter the term in the query field. 2. Click the **Pathway Enrichment icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-cadedf758605eac7f2f9cc88eecb6cfb254258af%2Fimage%20\(25\).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 **Pathway Enrichment icon** ![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-cadedf758605eac7f2f9cc88eecb6cfb254258af%2Fimage%20\(25\).png?alt=media). ## Understanding Biogroups Results Results are a ranked list of enriched biogroups. Each row shows the biogroup name, source, and enrichment score. ### Drilling into a Biogroup Click a biogroup name to see supporting studies broken down by organism and data type. Click **View Individual Studies** to see studies containing biosets that overlap with the biogroup and are tagged with your queried phenotype or compound. Expand a study to see biosets. Click a bioset to see: * **Venn diagram** — showing the overlap between your queried bioset (or concept-tagged biosets) and the biogroup. The p-value is the probability of the overlap occurring by chance. * **Feature list** — the genes in the overlap, with their statistics (fold change, p-value, etc.) * **Directional filter** — use the dropdown to show all genes, only up-regulated, or only down-regulated in the comparison. ## Venn Diagram Interpretation **If you queried with a bioset:** * Circle 1: genes in your queried bioset * Circle 2: genes in the correlated biogroup * Overlap: genes in both * p-value: probability of overlap by chance **If you queried with a phenotype or compound:** * The diagram shows the overlap between the biogroup and a bioset from a study tagged with your query term. ## Exporting Results * **Export Results** — downloads a list of all correlated biogroups. * **Export Data** — from within a specific biogroup, downloads the list of genes common to your bioset and that biogroup. * **Export Image** — downloads the Venn diagram and associated statistics. ## How Biogroups Differs from Other Enrichment Tools CE uses directional rank-based enrichment statistics that account for both the direction of regulation (up/down) and the rank of each gene within a bioset. For detailed methodology, see [Kupershmidt et al., 2010, *PLoS ONE*](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013066). --- # 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/biogroups.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.