> 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/release-notes.md). # Release Notes ## 2026 June 7 — Correlation Engine 2.9.0 ### New Features and Enhancements * High resolution bioset-bioset graphs * New single cell signatures for Body Atlas * Meta-Analysis file export and API result improvements * New filter options added to Atlases and Meta-Analysis ### Fixed Issues * Fixed an issue where facet filters would disappear and reappear when multiple facets clicked in Clinical Trials and Literature * Fixed an issue where the Knockdown Atlas did not include child genemode concepts with parent genemode concepts * Fixed an issue where Clinical Trials location pins were not present for newer trials * Fixed an issue where some exported data were in the wrong columns for somatic mutation and SNP GWAS datatypes ### Known Issues * None ### Data Content Updates | | Added since prior minor version release | Total public content | | ------- | --------------------------------------- | -------------------- | | Studies | 219 | 27,566 | | Biosets | 1,568 | 202,676 | Single cell biosets incorporated into Body Atlas: 3,287 *** ## 2026 March 25 — Correlation Engine 2.8.0 ### New Features and Enhancements * Single Cell types in Body Atlas app and Body Atlas API * Filtering of Correlated Disease by datatype and organism data in Disease Atlas * Filtering of Correlated Compounds by datatype and organism data in Pharmaco Atlas * Filtering of Perturbed Genes by datatype and organism data in Knockdown Atlas * Expanded number of results returned in Genetic Markers and Knockdown Atlas apps * Header updated to match new Illumina style and navigation to other applications * Import enhancement to enable both rank and fold change as statistical columns in the same bioset * Updated copyright year to 2026 ### Fixed Issues * Fixed an issue where import could not handle version number suffixes in import identifiers * Fixed an issue where import verify API failed to handle large numbers of biosets * Fixed an issue where macOS metadata in zipped files caused import to fail * Fixed an issue where *Macaca mulatta* and *Pan troglodytes* features were missing from GO taxonomy ### Known Issues * On Clinical Trials page, the location is not indicated on the map graphic for some trials * The correct location information is described in the text on the page * On Clinical Trials page, selecting a facet filter sometimes causes other facets to disappear * Click on Clear All Filters to restore the full facet list * For somatic mutation and SNP GWAS datatypes, some exported data are in the wrong columns * The data present are correct but formatted incorrectly ### Data Content Updates | | Added since prior minor version release | Total public content | | ------- | --------------------------------------- | -------------------- | | Studies | 210 | 27,347 | | Biosets | 1,747 | 201,108 | Biosets incorporated into Single Cell Body Atlas: 1,357 *** ## 2025 November 14 — Correlation Engine 2.7.0 ### New Features and Enhancements * Updates to MeSH (Medical Subject Headings) descriptions added * Enabled importing multiple biosets in a single API job * Enabled return of external identifiers to biogroups.api results * New public content ### Fixed Issues * None ### Known Issues * *Macaca mulatta* and *Pan troglodytes* biosets missing gene ontology biogroup matches ### Data Content Updates | | Added since prior minor version release | Total public content | | ------- | --------------------------------------- | -------------------- | | Studies | 405 | 27,137 | | Biosets | 2,974 | 199,361 | *** ## 2025 August 14 — Correlation Engine 2.6.1 ### Features and Enhancements * None ### Fixed Issues * Fixed an issue where bookmarks showed incorrect URL * Fixed an issue where sequence centric uploads required the selection of an experiment type * Fixed an issue that prevented protein-DNA binding and histone modification datatypes from being added to histogram visualizations in Meta-Analysis ### Known Issues * None *** ## 2025 June 16 — Correlation Engine 2.6.0 ### Features and Enhancements * Scatter plot visualization of bioset vs. bioset comparisons * Import now accepts feature identifiers with version numbers appended * Protein datatype added to the import API ### Fixed Issues * Fixed an issue where no studies were showing under the "Studies for" tab in Pathway Enrichment and data could not be exported * Fixed an issue where filters on Meta-Analysis/Bioset Results tab were not applied to export * Updated privacy link in the footer ### Known Issues * None ### Data Content Updates | | Added since prior minor version release | Total public content | | ------- | --------------------------------------- | -------------------- | | Studies | 1,108 | 26,731 | | Biosets | 9,458 | 196,387 | *** ## 2025 April 10 — Correlation Engine 2.5.2 ### Features and Enhancements * None ### Fixed Issues * Fixed an issue where recent clinical trial results were not showing * Fixed an issue where RNA-Seq study count was not showing for domains without domain libraries * Fixed an issue where the public QuickView page was under heavy crawl load * Fixed copyright year to 2025 on all web pages ### Known Issues * None *** ## 2025 February 25 — Correlation Engine 2.5.1 ### Features and Enhancements * None ### Fixed Issues * Fixed an issue where recent clinical trial results were not showing * Fixed an issue where RNA-Seq study count was not showing * Fixed an issue where admin console access was blocked * Fixed an issue where user groups were not indexed/updated ### Known Issues * None *** ## 2024 December 17 — Correlation Engine 2.5.0 ### Features and Enhancements * Scatter plot displays of individual bioset data * Updates to "What's New at Correlation Engine" * Export enabled for SNP and DNA sequence-centric bioset data * Display of RNA-Seq study counts on home page * Updated Terms and Conditions ### Fixed Issues * Fixed an issue where filtering by genes in Meta-Analysis failed to map synonyms * Fixed an issue where import returned a time-out error when under heavy workload ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 383 | 26,400 | | Biosets | 3,523 | 192,500 | First-time addition of single-cell RNA-seq data to the public library: | | Total public content | | ------------------- | -------------------- | | Single cell studies | 60 | | Single cell biosets | 2,417 | *** ## 2024 August 6 — Correlation Engine 2.4.0 ### Features and Enhancements * Heatmap displays of gene and biogroup Meta-Analysis results * Updates to "What's New at Correlation Engine?" ### Fixed Issues * Fixed an issue where study counts were mismatched in Disease Atlas * Fixed an issue where some import scoring jobs failed and required re-submission * Fixed an issue where deleted biosets still affected overall study ranks * Fixed an issue where some studies with the Alzheimer's disease tag were not categorized ### Known Issues * When searching by gene query on the Cell Lines tab in Body Atlas, some genes return no results in the expanded third level details ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 210 | 26,117 | | Biosets | 1,094 | 188,977 | *** ## 2024 February 12 — Correlation Engine 2.3.0 ### Features and Enhancements * Images of QC plot files associated with public studies now streamed to the UI * Updated "What's New?" section on home page * Updated copyright year to 2024 ### Fixed Issues * Fixed an issue where some GWAS studies had outdated URLs in their description ### Known Issues * When searching by some biosets in Disease Atlas, some concepts show incorrect counts on the 'Studies for Concept' tab * When searching by gene query on the Cell Lines tab in Body Atlas, some genes return no results in the expanded third level details ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 145 | 25,907 | | Biosets | 363 | 187,883 | *** ## 2023 November 28 — Correlation Engine 2.2.1 ### Features and Enhancements * Update to Frequently Asked Questions with additional information to explain minimum column requirements for import * New example files available in Import help ### Fixed Issues * Fixed an issue where some somatic mutation data in Body Atlas cell lines was missing from bioset queries * Fixed an issue where a user received a "Succeeded" and "Failed" import message, followed by a "Succeeded" import message, and then a duplicate empty study would appear beside the correct study * Fixed an issue where imported gene identifiers used by different platforms for different genes prevented identifying the correct platform for import * Fixed an issue where a public study showed the wrong associated files * Fixed an issue where autocomplete performance was slowed ### Known Issues * No reported issues ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 139 | 25,762 | | Biosets | 591 | 187,520 | *** ## 2023 August 28 — Correlation Engine 2.2.0 ### Features and Enhancements * Swagger integration for Application Programming Interfaces (APIs) * Updated FAQ * Updated Terms of Service * Pathway Viewer and Pathway Studio links deprecated * mSigDB collection 8 cell types addition * Note: New imports will show results with the new mSigDB collection. Older imports will show incomplete results while re-scoring against the new biogroups takes place over the next several weeks. ### Fixed Issues * Fixed an issue where "Edit description" from Action drop down in Curated Studies was disabled * Fixed an issue where data filter did not return cell line results when filtering for copy number or somatic mutations in Cell Lines – Body Atlas ### Known Issues * No reported issues ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 515 | 25,623 | | Biosets | 13,071 | 186,929 | *** ## 2023 March 7 — Correlation Engine 2.1.1 ### Features and Enhancements * Meta-Analysis API — programmatically access the Meta-Analysis app functionality * Send to email option for large data exports from the user interface * Security improvements * Updated copyright to 2023 ### Fixed Issues * Fixed an issue where non-human biogroup results were showing duplicate features * Fixed an issue where the region filter was not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors * Fixed an issue where export from Active Biogroups timed out in studies with more than 20 biosets * Fixed an issue where third-level bioset queries were making unnecessary redundant calls creating a delay * Fixed an issue where some concepts were not finding studies/biosets with the corresponding tag in Curated Studies ### Known Issues * Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas * Workaround: Browse for Body Atlas cell lines where CNV or SM data is present and open individual datasets to inspect * 'Edit description' from Action drop down in Curated Studies temporarily disabled * Workaround: Load Study Inspector and click 'Edit description' button ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 328 | 25,108 | | Biosets | 7,841 | 173,858 | *** ## 2022 September 2 — Correlation Engine 2.1.0 ### Features and Enhancements * Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) enabled as a new supported datatype * Import Data Page help updated with guidelines and example files for ATAC-seq import * Boolean search for ATAC-seq data enabled ### Fixed Issues * Fixed an issue where on first upload of a bioset with a new concept tag, the tag category could not be found in Pathway Enrichment when searched for by same tag * Fixed an issue where the count of studies found by concept tag in Pathway Enrichment was not updated after new study import * Fixed an issue where studies in Curated Studies could not be found by compound tag Iniparib * Fixed an issue where there was an intermittent error on import mapping step when lift-over was applied * Fixed an issue where there was an intermittent interruption of import resulting in some or all missing biosets ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 184 | 24,780 | | Biosets | 7,764 | 166,017 | *** ## 2022 May 18 — Correlation Engine 2.0.6 ### Features and Enhancements * Import API extended to support all datatypes, now in addition to RNA-Expression: * Protein-DNA binding (ChIP-seq) * Methylation * SNP/GWAS * Copy number variation * Somatic Mutation * miRNA expression * Protein expression * Security and performance improvements * News feature removed due to discontinued RSS feeds ### Fixed Issues * Fixed an issue where searching Cell Line Body Atlas by certain Biogroups and viewing by rank returned an error * Fixed an issue where the owner's name of public studies was not properly appearing ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 164 | 24,596 | | Biosets | 751 | 158,253 | *** ## 2022 March 15 — Correlation Engine 2.0.5 ### Features and Enhancements * Updated copyright year to 2022 * Added 'single cell' as filterable sample source under advanced filter * Back-end updates to import process: * Extended database capacity * Updated APIs to improve performance of data transfer during import * Updated wording on licensing page * Security and performance improvements ### Fixed Issues * Fixed an issue where no warning message was given when a user tried to delete a group * Fixed an issue where second-level details of a study with hundreds or more biosets failed to expand when searching by gene * Fixed an issue where synonyms could not be deleted in ontology * Fixed an issue where studies did not show in certain categories (e.g., Olaparib) * Fixed an issue where the Clinical Trials map was not displaying properly * Fixed an issue where graphs in Meta-Analysis/Biogroups did not appear correctly when p-values were extremely small * Fixed an issue in Boolean Search where some genes were missing from autocomplete ### Data Content Updates | | Added since prior release | Total public content | | ------- | ------------------------- | -------------------- | | Studies | 1,597 | 24,549 | | Biosets | 2,419 | 157,558 | *** ## 2021 December 14 — Correlation Engine 2.0.4 ### Features and Enhancements * Added notification to ask user to review automated platform selection at 'review and submit' step of import * Enhanced Import REST API to support inclusion of supplemental report files * Enhanced Biosetfeatures REST API to include option to return normalized rank score shown in Meta-Analysis * Updates to improve import performance and provide improved feedback to user * Security and performance improvements ### Fixed Issues * Fixed an issue where async import failed to write complete information to database * Fixed an issue where the wrong default platform was pre-selected during import * Fixed an issue where obsolete custom platforms appeared in drop down at mapping step * Fixed an issue where the count of features displayed during data mapping import step differed from actual number of features in imported biosets * Fixed an issue where some biogroups were missing from Body Atlas Cell Lines page * Fixed an issue where biosets imported on NGS platforms mapped a small number of genes incorrectly * Fixed an issue where bioset-bioset queries timed out and failed to load when very large biosets were compared *** ## 2021 September 7 — Correlation Engine 2.0.3 ### Features and Enhancements * Added position verification checks on all genome builds. Genomic coordinates outside the range of known possible genomic coordinates will be dropped from uploads with a warning message to user * miRNA features updated from mirBase16 to mirBase22 * \~2–3× increase in number of miRNA features, depending on reference genome * Up to 20× increase in miRNA-gene target linkages, depending on reference genome * Security and performance improvements ### Fixed Issues * Fixed issue where miRNA import was disabled; public and private miRNA content have been reimported with updated feature information * Fixed an issue where new imported studies were missing from concept search results in Pathway Enrichment * Fixed an issue where study indexing failed intermittently * Fixed an issue where the EULA conflicted with single sign-on and IP restriction *** ## 2021 February 16 — Correlation Engine 2.0.2 ### Features and Enhancements * OMIM datasets have been updated to provide latest disease-gene associations * New L1000 Connectivity Map datasets added to public library, providing new chemical and genetic perturbation gene expression datasets ### Fixed Issues * Fixed an issue where non-human species datasets were not available when browsing MsigDB biogroups * Fixed an issue where genome build conversion was disabled (current accepted genome builds restored) * Fixed an issue where the Literature App did not update daily * Fixed an issue where `.xlsx` format documents were not supported for import * Fixed an issue where 'Request a study' was disabled * Fixed an issue where files associated to a study were not accessible in the UI (Enterprise accounts only) * Security updates *** ## 2020 November 4 — Correlation Engine 2.0 ### Features and Enhancements * Deployment of application to Amazon Web Services (AWS) * Gene model updates: Entrez 2018-01-01, GenBank v224, RefSeq v87, UniProt 2018-01, Homologene v68, MGI Vertebrate Homology 2018-02 * Biogroup updates based on: Gene Ontology 2018-07-23, MsigDB v6.2 (updated canonical pathways and positional gene sets; added hallmark gene sets, chemical and genetic perturbations, cancer gene neighborhoods, cancer modules, oncogenic signatures, immunologic signatures), InterPro v69 * Gene expression platform technology updates: 128 existing platforms refreshed, 15 new platforms added ### Fixed Issues * Security fixes * Browser back button did not properly refresh page in any atlas * Biogroup Size filter was not applied when exporting bioset-biogroup search results --- # Agent Instructions This documentation is published with GitBook. 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