Release Notes

2024 August 06 - Correlation Engine v2.4.0

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 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 v2.3.0

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

  • Update 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  • Fixed an issue where some GWAS studies had outdated URLs in their description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 v2.2.1

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 that are used by different platforms for different genes prevented identifying correct platform for import

  • Fixed 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 v2.2.0

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 Ac tion 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 muttions 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 v2.1.1

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 by adding option to email results of very large export requests

  • 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

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: 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 v2.1.0

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 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 applied

  • Fixed an issue where there was an intermittent interruption of import resulting in some or all missing biosets

Known Issues

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

Data Content Updates

Added since prior release
Total Public Content

Studies

184

24,780

Biosets

7,764

166,017

2022 May 18 - Correlation Engine v2.0.6

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 owner’s name of public studies not properly appearing

Known Issues

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

Data Content Updates

Added Since Prior Release
Total Public Content

Studies

164

24,596

Biosets

751

158,253

2022 March 15 - Correlation Engine v2.0.5

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 user tries to delete a group

  • Fixed an issue where second level details of a study with hundreds or more biosets failed to expand where 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 gene were missing from autocomplete

Known Issues

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

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 v2.0.4

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 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

Known Issues

  • Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

  • Clinical Trials map feature temporarily disabled

Data Content Updates

Added Since Prior Release
Total Public Content

Studies

  • Cosmic Cancer Tissues

  • Cosmic Cell Lines

  • L1000 Connectivity MAP

621

  • 46

  • 22

  • 21

22,900

Biosets

  • Cosmic Cancer Tissues

  • Cosmic Cell Lines

  • L1000 Connectivity MAP

20,189

  • 3,697

  • 478

  • 13,837

155,254

2021 - September 07 - Correlation Engine v2.0.3

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

    • ~2-3X increase in number of miRNA features, depending on reference genome

    • Up to 20X increase in miRNA-gene target linkages, depending on reference genome

  • Security and performance improvements

Upcoming Changes

  • Old URLs of nextbio.com & *.ussc.informatics.illumina.com will be retired September 2021.

Fixed Issues

  • Fixed issue where miRNA import was disabled o Public and private miRNA content have been reimported with updated feature information, as described in Features section

  • 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

Known Issues

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas o Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bioset inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

  • Clinical Trials map feature temporarily disabled

Data Content Updates

  • With the introduction of Correlation Engine v2.0, 90% of all the public curated studies were migrated to the 2.0 application.

Not Migrated to v2
V1 Original Content

Studies

1,744

23, 607

Biosets

8,097

142,539

  • The following shows the running total of content including studies new to v2

Added Since v2.0 Release
Total Public Content

Studies

1,240

22,668

Biosets

18,580

149,211

  • Going forward, Correlation Engine public data additions will be primarily focused on the newest data appearing in Gene Expression Omnibus. Users are encouraged to use the request a study feature under Curated Studies/ All studies to submit Geo Series (GSE) id or PMID will links to the public available data

2021 February 16 - Correlation Engine v2.0.2

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

    • New non-human uploads will be indexed against all biogroups

    • Previously uploaded non-human datasets will be indexed over the next 2 weeks

  • Fixed an issue where genome build conversion was disabled. (As a result, datasets based on genomic coordinates can only be accepted from NCBI build 36/UCSC hg18, NCBI build 37/UCSC mm9, NCBI RGSC v3.4/UCSC rn4, NCBI WS190/UCSC ce6, NCBI release 5.2.UCSC dm3, NCBI build 2.1/UCSC sacCer2, NCBI build 1.1/UCSC rheMac2, NCBI build 2.1/UCSC galGal3, NCBI build 2.1/UCSC panTro2, NCBI Btau_4.0/UCSC bosTau4, NCBI Zv8/UCSC danRer6, NCBI build 2.1/UCSC canFam2.) Currently accepted builds are now:

    • GRCh38 | UCSC hg38

    • GRCh37 | UCSC hg19

    • NCBI 36 | UCSC hg18

    • NCBI 35 | UCSC hg17

    • NCBI 34 | UCSC hg16

    • GRCm38 | UCSC mm10

    • GRCm37 | UCSC mm9

    • NCBI build 36 | UCSC mm8

    • NCBI RGSC v3.4 | UCSC rn4

    • ILMN-ce6 | UCSC ce6

    • ILMN-ce4 | UCSC ce4

    • ILMN-ce2 | UCSC ce2

    • ILMN-dm6 | UCSC dm6

    • NCBI release 5.2 | UCSC dm3

    • ILMN-dm2 | UCSC dm2

    • R64-1-1 | UCSC sacCer3

    • R61-1-1 | UCSC sacCer2

    • R27-1-1 | UCSC sacCer1

    • NCBI build 1.1 | UCSC rheMac2

    • NCBI build 2.1 | UCSC galGal3

    • NCBI build 2.1 |UCSC panTro2

    • NCBI Btau_4.0 | UCSC bosTau4

    • NCBI Zv8 | UCSC danRer6

    • NCBI build 2.1 | UCSC canFam2

  • Fixed an issure where 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 UI (Enterprise accounts only)

  • Security Updates

Known Issues

  • miRNA dataset import temporarily disabled

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bio set inspectors

  • ‘Edit description’ from Action drop down in Curated Studies temporarily disabled

    • Work around: Load Study Inspector and click ‘Edit description’ button

  • Clinical Trials map feature temporarily disabled

  • Intermittently, newly imported studies to domain libraries not indexed in Pathway Enrichment when search by tagged concept.

    • Workaround: User can edit study name or description and save to trigger re-indexing. Alternatively, search by bioset in Pathway Enrichment to find associated biogroups

2020 November 04 - Correlation Engine v2.0

Features and Enhancements

  • Deployment of application to Amazon Web Serves (AWS)

  • Gene models have been updated to the following versions:

  • Entrez 2018-01-01

  • GenBank v224

  • RefSeq v87

  • UniProt 2018-01

  • Homologene v68

  • MGI Vertebrate Homology 2018-02

  • Biogroups have been updated based on the following resources:

    • Gene Ontology 2018-07-23

    • MsigDB v6.2

      • Updated

        • Regulatory motifs

        • Canonical pathways

        • 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 with revised feature-mapping information

    • 15 new gene expression platforms supported

      • Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip

      • Affymetrix Human Gene Expression Array - PrimeView

      • Affymetrix Human Gene 2.0 ST Array - HuGene-2_0-st - transcript (gene) version

      • Affymetrix Human Transcriptome Array 2.0 - HTA-2_0 - transcript (gene) version

      • Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version)

      • Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)

      • Affymetrix Mouse Gene 2.1 ST Array [transcript (gene) version]

      • Affymetrix Mouse Gene 2.0 ST Array [transcript (gene) version]

      • Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version)

      • Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Feature Number version)

      • Affymetrix Rat Gene 1.0 ST Array [transcript (gene) version]

      • BioSpyder TempO-Seq

      • Custom Human

      • Custom Mouse

      • Custom Rat

      • Agilent-072363 SurePrint G3 Human GE v3 8x60K array (Feature Number version)

      • Agilent-072363 SurePrint G3 Human GE v3 8x60K array (Probe Name version)

Fixed Issues

  • Security Fixes

  • Browser back button does not properly refresh page in any atlas

  • Biogroup Size filter not applied when exporting bioset-bigroup search results

Known Issues

  • Genome build conversion is temporally disabled. As a result, datasets based on genomic coordinates can only be accepted from NCBI build 36/UCSC hg18, NCBI build 37/UCSC mm9, NCBI RGSC v3.4/UCSC rn4, NCBI WS190/UCSC ce6, NCBI release 5.2.UCSC dm3, NCBI build 2.1/UCSC sacCer2, NCBI build 1.1/UCSC rheMac2, NCBI build 2.1/UCSC galGal3, NCBI build 2.1/UCSC panTro2, NCBI Btau_4.0/UCSC bosTau4, NCBI Zv8/UCSC danRer6, NCBI build 2.1/UCSC canFam2

  • miRNA dataset import temporarily disabled

  • Non-human species datasets temporarily not available when browsing some MsigDB biogroups.

  • Data filter does not return cell line results when filtering for copy number or somatic mutations in Cell Lines - Body Atlas

    • Work around: Browse for Body Atlas cell lines where CNV or SM data is present and open up individual datasets to inspect

  • Export from Active Biogroups times out in studies with more than 20 biosets

    • Work around: Add biosets to Meta-analysis in smaller batches and export from Biogroup Results tab in Meta-analysis

  • Region filter temporarily not present for Histone Ubiquitination, Histone Acetylation, Histone Methylation bio set inspectors

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