> 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/querying-results.md). # Querying Overview Correlation Engine provides ten specialized applications ("apps") for exploring the relationship between your data and the global corpus of genomic experiments. All apps are accessible from the **app menu** at the top of every CE page. ## Query Entry Points There are three ways to initiate a query in any CE app: ### 1. Gene, Concept, or Keyword Text Search Type a term into the query field and press the app icon for the app you want to query. Accepted term types: * **Genes / SNPs** — HGNC symbols, Entrez Gene IDs, RefSeq IDs, Ensembl IDs, dbSNP rs IDs * **Phenotypes / Diseases** — SNOMED-CT terms (e.g., "breast cancer", "Alzheimer disease") * **Tissues** — MeSH tissue terms (e.g., "liver", "cerebral cortex") * **Compounds** — MeSH and PubChem compound names (e.g., "tamoxifen", "dexamethasone") * **Biogroups** — Gene Ontology terms, MSigDB pathway names, InterPro protein families {% hint style="info" %} The **auto-complete** drop-down suggests recognised terms as you type. Selecting from auto-complete ensures the term is mapped correctly to CE's ontology. You can also type freely and press Enter to search without selecting from auto-complete. {% endhint %} ### 2. Bioset Query A bioset query uses your entire experimental dataset (a ranked list of genes with statistics) as the input to an app, rather than a single gene or concept. To query with a bioset: 1. Find a bioset of interest — from **My Studies**, within expanded app results, or by browsing **Curated Studies**. 2. 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 the bioset name. 3. Click the icon for the app you want to query. App icons also appear next to bioset names and correlated results throughout CE — clicking them launches a query with that item as input. ### 3. Sequence Region Query To query by genomic coordinates: 1. Click the **"Search sequence regions"** link next to the query button. 2. Choose an organism and chromosome. 3. Enter start and stop coordinates (region must be < 10 million bases). 4. Click the app icon to query. Sequence region queries are supported by: QuickView, Curated Studies, Disease Atlas, Pharmaco Atlas, Knockdown Atlas, and Genome Browser. *** ## How CE Scores and Ranks Results CE uses proprietary rank-based statistical algorithms to score correlations. The process works in two stages: 1. **Bioset-level scoring** — CE identifies individual biosets in which your query term (or a gene/feature from your bioset) is statistically significant. Each bioset receives a score based on the rank and significance of the query term within it. 2. **Categorization** — Correlated biosets are grouped by category (disease, tissue, compound, perturbed gene, or biogroup). CE applies corrections for multiple hypothesis testing and assigns a normalised score of **100** to the top result, with all other results normalised relative to it. {% hint style="warning" %} A low normalised score does **not** mean a result is statistically non-significant — it means it is less significant relative to the top-ranked result. Low-scoring results may still have real biological relevance. {% endhint %} *** ## The Apps | App | Query Input | What It Returns | | ------------------------------------------------------------------------------------------- | -------------------------------------------- | ----------------------------------------------------- | | [QuickView](/correlation-engine/querying-and-interpreting-results/quickview.md) | Gene, SNP, concept, region, biogroup, bioset | Summary of all CE data for the query term | | [Curated Studies](/correlation-engine/querying-and-interpreting-results/curated-studies.md) | Gene, concept, keyword, bioset, region | Ranked list of individual studies | | [Body Atlas](/correlation-engine/querying-and-interpreting-results/body-atlas.md) | Gene, biogroup, bioset, tissue/cell line | Tissues, cell types, cell lines ranked by expression | | [Disease Atlas](/correlation-engine/querying-and-interpreting-results/disease-atlas.md) | Gene, SNP, region, biogroup, bioset | Diseases ranked by statistical correlation | | [Pharmaco Atlas](/correlation-engine/querying-and-interpreting-results/pharmaco-atlas.md) | Gene, region, biogroup, bioset | Compounds and treatments ranked by correlation | | [Knockdown Atlas](/correlation-engine/querying-and-interpreting-results/knockdown-atlas.md) | Gene, region, biogroup, bioset | Perturbed genes whose knockdown correlates with query | | [Biogroups](/correlation-engine/querying-and-interpreting-results/biogroups.md) | Bioset, phenotype, compound | Enriched Gene Ontology, MSigDB, InterPro sets | | [Meta-Analysis](/correlation-engine/querying-and-interpreting-results/meta-analysis.md) | Up to 150 biosets | Consensus gene signatures and correlated biogroups | | [Literature](/correlation-engine/querying-and-interpreting-results/literature.md) | Gene, concept, keyword | PubMed publications with tag-cloud filtering | | [Clinical Trials](/correlation-engine/querying-and-interpreting-results/clinical-trials.md) | Gene, concept, keyword | ClinicalTrials.gov entries with tag-cloud filtering | *** ## Supported Data Types Abbreviations When browsing results, supporting data type columns display abbreviations. Hover over any abbreviation in the UI to see its full name, or refer to the table below. | Code | Data Type | | ---- | ------------------------------ | | RE | RNA Expression | | MI | miRNA Expression | | ME | DNA Methylation | | PD | Protein-DNA Binding (ChIP-seq) | | CN | DNA Copy Number | | SM | Somatic Mutation | | GT | SNP / GWAS | | AT | ATAC-seq | | PE | Protein Expression | | MU | Mutations / Phenotypic | | DT | Therapeutic | | HA | Histone Acetylation | | HM | Histone Methylation | | HU | Histone Ubiquitination | | GM | Germline Mutation | --- # 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/querying-results.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.