> 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/reference/faq.md). # FAQ This page covers frequently asked questions organized by topic. For app-specific how-to guidance, see the [Querying and Interpreting Results](/correlation-engine/querying-and-interpreting-results/querying-results.md) section. *** ## General FAQs ### How do I query an app? Correlation Engine applications ("apps") can be accessed from the app menu at the top of every CE page. 1. Go to the top of any page within Correlation Engine. 2. Enter your term in the query field (under the app menu). 3. Click the icon for the app you want to query. If you're already viewing results for a query term, click any app icon to re-query with the same term in that app. ### How do I query an app with a bioset? 1. Find a bioset of interest (in My Studies, from expanded app results, or in 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 next to gene or concept names in results — clicking them launches a query with that specific item. ### How do I query an app with a sequence region? 1. Click the **"Search sequence regions"** link next to the query button. 2. Choose an organism and chromosome from the drop-down menus. 3. Enter the start and stop coordinates (region must be less than 10 million bases). 4. Click the icon for the app you want to query. Click **"Go back to main search"** to return to text-based querying. Sequence region queries are supported by: QuickView, Curated Studies, Disease Atlas, Pharmaco Atlas, Knockdown Atlas, and Genome Browser. ### How does Correlation Engine determine the content of query results? CE apps use public and private experimental data as their sources — not PubMed or other literature sources (Literature and Clinical Trials are exceptions). This means you can potentially discover associations not yet well-supported in published research. For example, querying Disease Atlas with a gene returns diseases correlated with that gene based on experimental studies in which the gene had a significant result, not based on what has been written about the gene. ### What are Correlation Engine's data sources? **Data correlations:** * [Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/) * [Array Express](https://www.ebi.ac.uk/arrayexpress/) * [Stanford Microarray Database](http://smd.stanford.edu/) * [The Cancer Genome Atlas](https://cancergenome.nih.gov/) * [OMIM](https://www.ncbi.nlm.nih.gov/omim) * Manually curated studies from published literature **Gene/SNP identifiers:** Entrez Gene, UniGene, Ensembl, RefSeq, GenBank, dbSNP **Cross-species orthologs:** Mouse Genome Informatics, HomoloGene, Ensembl **Ontologies for semantic tagging:** * Phenotypes: SNOMED® Clinical Terms * Tissues: MeSH * Compounds: MeSH and PubChem * Biogroups: Gene Ontology, MSigDB, InterPro, TargetScan * Organisms, Authors: MeSH, PubMed ### How are Correlation Engine results scored and ranked? CE uses proprietary algorithms to calculate and rank results: 1. CE identifies individual biosets significantly correlated with your query term. 2. Based on statistical significance, it ranks all studies containing correlated biosets. 3. Correlated studies are grouped by category (disease, tissue, compound, etc.) — this is "categorization." 4. Additional statistical criteria, including correction for multiple hypothesis testing, are applied. 5. The top-ranked result receives a score of 100; all other results are normalised relative to it. For Disease Atlas, the ranking considers: 1. Total number of disease-specific studies in which the query term was measured 2. Number of disease-specific studies in which the query term was found significant 3. Ranks of the query term in each disease study 4. Consistency of the association across disease studies For detailed methodology, see: [Kupershmidt et al., 2010, *PLoS ONE*](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013066). ### Is a low-scoring result non-significant? No. CE scores all results relative to the top-ranked result (score = 100). A low-scoring result may have less statistical significance relative to the top result, but it can still have real biological relevance. ### What do the Venn diagrams in expanded results mean? The Venn diagram shows: * How many genes are in your queried bioset or biogroup * How many genes are in the correlated bioset or biogroup * How many genes are in both The p-value is the probability that such an overlap would occur by chance if there were no biological link between the two sets. ### What are the scatter plots in expanded results? When both biosets in a comparison have applicable statistical data, a scatter plot button appears. A common use is to plot fold change vs. -log(p-value) (Volcano plot) to show co-activity between two datasets. The first recognised statistical column in each bioset is selected by default. Use the drop-down menus to change axes and click **Generate new plot**. ### What do the abbreviations in the Supporting Data Types column mean? | Code | Data Type | | ---- | ---------------------- | | AT | ATAC-seq | | CN | DNA Copy Number | | DT | Therapeutic | | GM | Germline Mutation | | GT | SNP GWAS | | HA | Histone Acetylation | | HM | Histone Methylation | | HU | Histone Ubiquitination | | ME | DNA Methylation | | MI | miRNA Expression | | MU | Mutations / Phenotypic | | PD | Protein-DNA Binding | | RE | RNA Expression | | SM | Somatic Mutation | Hover over any abbreviation in the UI to see its full name. *** ## QuickView FAQs ### What is QuickView? QuickView provides a rapid top-level summary of all CE data for a gene, SNP, sequence region, biogroup, bioset, phenotype, tissue, or compound. It shows top results from each app, top correlated studies, top literature hits, and top clinical trial matches. ### What can my QuickView results tell me? **Correlation Engine Summary tab:** * Top 5 data correlations from each relevant CE app * Top 5 correlated studies from Curated Studies * Top 5 hits from Literature * Top 5 hits from Clinical Trials **General Info tab:** * Compiled from PubMed, Gene Ontology, dbSNP, PubChem, MSigDB, and other public sources * For genes: alternate names, orthologs, transcription factor binding sites, GO and pathway membership ### What is the purpose of the Scatter Plot in QuickView for a bioset? The scatter plot displays the statistical columns from the bioset. A typical use is fold change on the x-axis vs. -log(p-value) on the y-axis (Volcano plot). System-recognised p-values and q-values are log-transformed and added as axis options in the drop-downs. *** ## Curated Studies FAQs ### What is Curated Studies? Curated Studies lets you browse or query all datasets you or Correlation Engine have imported. Results are flat ranked lists of individual studies — unlike atlas apps that categorize results. ### What kinds of query terms can I use with Curated Studies? * **Genes, SNPs, regions, biogroups, biosets:** Ranked list of studies correlated with the query term. * **Concepts (phenotypes, tissues, compounds):** List of studies tagged with or mentioning the concept. * **Keywords:** Text-based search across study names and descriptions. * **No query:** Browse all studies using the All Curated Studies button. ### How does Curated Studies differ from other apps? Results from Curated Studies are only lists of individual studies — not categorized or grouped. Disease Atlas groups by disease; Genetic Markers groups by gene or SNP. Use Curated Studies to inspect raw correlated studies or find negative results. ### How do I see the statistics for a specific bioset? 1. Click a study title to reveal the correlated biosets. 2. Click a bioset title to see the per-feature statistics (fold change, p-value, copy number change, etc.). *** ## Body Atlas FAQs ### What is Body Atlas? Body Atlas maps normalised gene expression across tissues, cell types, cell lines, stem cells, and single-cell populations. A gene, biogroup, or bioset query returns tissues ranked by relevance; a tissue or cell line query returns genes ranked by expression level. ### What tissues and cell types are covered? Microarray-based: * 128 human tissues, 170 human cell types, 748 human cell lines, 52 stem cell types * 151 mouse tissues, 409 mouse cell types GTEx RNA-seq: 50 human tissues from 505 RNA-seq samples Single-cell (v2.8+): 1,186+ cell types from over 1,357 scRNA-seq analyses ### What are the different ways to view Body Atlas results? * **By body system (default):** grouped into anatomical systems * **By rank:** sorted by expression or correlation score For tissue/cell line queries, view tissue-specific expression, or for cell lines, somatic mutations and copy number changes. *** ## Disease Atlas FAQs ### What is Disease Atlas? Disease Atlas finds diseases, traits, conditions, and surrogate endpoints correlated with a gene, SNP, sequence region, biogroup, or bioset. Results are grouped by disease category and ranked by statistical significance. ### What kinds of query terms can I use with Disease Atlas? Genes, SNPs, sequence regions, biogroups, and biosets. Disease Atlas does not accept disease names as input — to find studies for a disease, use Curated Studies. ### Why is the number of studies shown in Correlated Diseases different from the Studies For... tab? Studies in the Studies For... tab may be excluded from Correlated Diseases if they fail additional categorization significance thresholds (e.g., multiple hypothesis testing correction). Private studies appear in Studies For... but are not included in categorization (unless you are an Enterprise user with domain library studies). *** ## Pharmaco Atlas FAQs ### What is Pharmaco Atlas? Pharmaco Atlas finds compounds and treatments significantly correlated with a gene, sequence region, biogroup, or bioset. Results are ranked by statistical significance. ### What kinds of query terms can I use with Pharmaco Atlas? Genes, sequence regions, biogroups, and biosets. Pharmaco Atlas does not accept compound names as input — to find studies for a compound, use Curated Studies. *** ## Knockdown Atlas FAQs ### What is Knockdown Atlas? Knockdown Atlas finds genes whose genetic perturbation (knockdown, knockout, or overexpression) significantly affects your query term. It is like performing a reverse genetic perturbation experiment. ### Why is the app called Knockdown Atlas if it includes overexpression studies? Knockdown Atlas shows results from any genetic perturbation experiment — knockout, gene silencing, and overexpression — but knockdowns and knockouts are the predominant type covered. ### How do I find all genes affected by perturbing a specific gene? Query Curated Studies, filter by the gene name as a keyword, then use the Advanced filter to check **Mutant vs. wildtype** in the Experiment Design menu. *** ## Biogroups FAQs ### What is Biogroups? Biogroups (also called Pathway Enrichment) shows canonical gene sets significantly enriched in a queried bioset or associated with a phenotype or compound. Biogroups come from Gene Ontology, MSigDB, InterPro, and TargetScan. ### What does "biogroup" mean? A biogroup is a named collection of genes associated with a biological function, pathway, protein family, or regulatory motif. No numerical information is directly associated with a biogroup. ### How do I find out which biogroups a gene belongs to? Query QuickView with the gene name, then click the **General Info** tab and scroll to the Gene Ontology, Pathways, and Protein Family biogroups at the bottom of the page. ### How does Biogroups compare to other pathway enrichment tools? CE uses directional rank-based enrichment statistics that account for direction (up/down regulation) and rank. See [Kupershmidt et al., 2010, *PLoS ONE*](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013066) for methodology details. *** ## Literature FAQs ### What is the Literature app? Literature shows PubMed publications matching your query term, with tag-cloud filtering extracted from abstracts. CE indexes over 19 million abstracts and 130,000 full-text articles from PubMed Central. ### What is a tag cloud? A tag cloud displays key biomedical terms extracted from your search results. Tags are listed alphabetically; larger typeface indicates stronger association with your query term. Click any tag to filter results. *** ## Clinical Trials FAQs ### What is Clinical Trials? Clinical Trials shows entries from [ClinicalTrials.gov](https://clinicaltrials.gov/) matching your query, with tag-cloud filtering from trial descriptions. Results come from text-based searches, not genomic data correlations. *** ## Search-Related Questions ### What does the Studies & Projects page display? The Studies & Projects section shows studies accessible according to your permissions: your studies, studies accessible through shared projects, public studies, or all studies. ### How does the auto-complete function work? Auto-complete provides a drop-down list of recognised genes, pathways, tissues, authors, SNPs, and biomedical concepts as you type, using biological and medical ontologies and proprietary heuristics. Auto-complete is optional — you can type a term and press Enter without selecting from the drop-down. ### How does filtering of results work? On Data Correlations pages, use organism, data type, and keyword filters to narrow results. Within text-based search results (Literature, Clinical Trials), enter any term in the filter box to narrow results. *** ## Data Import Questions ### What column headers should I have in my data? The system looks for required key column labels. For gene/protein expression, the identifier column header can be `gene`, `accession`, `symbol`, `protein`, etc. For sequence-centric data, the first columns are `chr`, `start`, `stop`. For SNP/GWAS, the header is `snp`. The identifier column must be the leftmost column, or must have the header `Gene name`. ### What is the acceptable data format? Text (`.txt`), `.csv`, or Excel (`.xls`, `.xlsx`) files. Standard statistical columns recognised: fold change, log2 fold change, p-value, q-value, score, rank, correlation. Up to 5 custom numeric columns allowed. ### What type of gene and protein identifiers does CE support? NCBI Gene IDs, gene symbols, NCBI accession numbers, Ensembl IDs, RefSeq identifiers, IPI IDs, UniGene IDs, dbSNP IDs, and probe IDs from most Affymetrix, Illumina, Agilent, and GE Healthcare platforms. ### Can I import multiple files as a zip archive? Yes, up to 35 MB per file. When using macOS zip tools, ensure hidden OS files (e.g., `.DS_Store`) are not included. ### Can I import my own data privately? Yes, as a Correlation Engine Professional or Enterprise user you can upload, save, and correlate your own data with public data. ### Why should I tag my data? Tagging significantly improves search results, enables your study to appear in categorized atlas results, and helps colleagues understand the biological context. Each study should be tagged with: tissue/cell line, phenotype (if applicable), and genetic or chemical modifications. ### How does CE rank features during import? CE selects the ranking column in this order: fold change → p-value → score → rank. If using fold change, log₂ and 0-N values are converted to ±fold change on upload. ### How can I bring in results from BaseSpace applications? See the detailed conversion guides: * [Cufflinks Assembly & DE output](/correlation-engine/reference/faq/cufflinks-output.md) * [RNA-Express output](/correlation-engine/reference/faq/rna-express-output.md) * [RNA-Seq Alignment output](/correlation-engine/reference/faq/rna-seq-alignment.md) * [BaseSpace ChIP-Seq output](/correlation-engine/reference/faq/basespace-chip-seq.md) *** ## Meta-Analysis Questions ### What is Meta-Analysis? Meta-Analysis enables users to query with a collection of up to 150 biosets to derive a consensus gene signature and discover commonly regulated biogroups. It identifies the most consistently and highly regulated genes across multiple biosets. ### How do I run Meta-Analysis? Click the Meta-Analysis icon next to biosets of interest (anywhere in CE) to add them. When ready, click the large Meta-Analysis icon in the app menu, review the setup, and click Run. ### What can I put into Meta-Analysis? Up to 150 biosets spanning different platforms, organisms, projects, and libraries. ### How do you compute the most significant genes? The two most important parameters are: (1) the activity level of a gene in each bioset, and (2) the specificity — the number of biosets in which the gene is active. ### How do I interpret the score matrix? Each bar height represents the correlation score between the queried bioset and the result. Red bars above midline = positive directional correlation; green bars below midline = negative directional correlation; orange bars = non-directional correlation (SNPs/mutations). Absent bar = non-significant correlation. *** ## Library-Related Questions ### What is the Public Domain Library? The Public Library contains all CE-curated public studies. Content cannot be edited by users. ### What is the Domain/Company Library? The Domain Library contains studies proprietary to your organisation. Only users within your domain have access. Promoting studies to domain-wide visibility requires administrator permission. *** ## Enterprise-Related Questions ### Is our data secure on Correlation Engine Enterprise? Yes. Illumina's ISO 27001–certified security program covers CE. Key features include full audit trails, TLS 1.2 encryption in transit, AES-256 encryption at rest, and automated data integrity checks. See the [Illumina Data Security and Privacy Statement](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/data-security-privacy-statement-m-gl-00709/data-security-privacy-statement-m-gl-00709.pdf). ### How can our organisation upload studies in bulk? CE provides APIs for programmatic bulk import. Contact . ### Does Correlation Engine provide APIs? Yes. APIs are available for querying data in and returning results out of CE. Contact for documentation. ### How can we control data sharing among groups? Each user can create private groups and share data only with members of those groups. Data sharing within an organisation can be managed through domain library access controls. ### Can we keep some data private from other users in our organisation? Yes. Use group-level sharing controls. By default, imported studies are private. Domain-wide promotion requires an explicit administrator action. --- # 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/reference/faq.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.