In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Version 1.4.2

• Date: 2023-08-16

Changed

• Data updates
• WikiPathways (20230810)
• COMPARTMENTS (2023-08)
• KEGG (20230710)
• BioGRID (v4.4.224)
• Open Targets Platform (2023.06)
• Upgraded sigven/phenOncoX to v0.6.3:
  • Experimental Factor Ontology (v3.56.0)
  • Human Disease Ontology (2023-07-20)

• A limited set of TCGA amplifications/deletions were erroneously left out in v1.4.1 (gene alias matching) - fixed in v1.4.2

• Functionality

• Updated Citation Note sections in report
• Fixed some typos in the report template

Version 1.4.1

• Date: 2023-06-18

Changed

• Data updates
• TCGA (20220329 - v37.0)
• WikiPathways (20230610)
• CancerMine (v50, 20230301)
• COMPARTMENTS (2023-05)
• KEGG (20230330)
• BioGRID (v4.4.222)
• Open Targets Platform (2023.02)
• Cancer Gene Census (v98)
• Network of Cancer Genes (v7.1)
• MSigDB (v2023.1.Hs)

• Upgraded sigven/phenOncoX to v0.6.1:

  • Experimental Factor Ontology (v3.54.0)
  • Human Disease Ontology (2023-05-31)

• Functionality

• Added Citation Note section for each output module - key citations
• Added data licensing terms in Documentation & Settings module

Version 1.4.0

• Date: 2023-02-21

Changed

• Data updates
• TCGA (20221212 - v36.0)
• WikiPathways (20230210)
• CancerMine (20230114)
• COMPARTMENTS (2023-01)
• KEGG (20230101)

• Upgraded sigven/phenOncoX to v0.5.6:

  • Experimental Factor Ontology (v3.50.0)
  • Human Disease Ontology (2023-01-31)

• Functionality

• Loading of databases
  • Downloading through Google Drive can somethis cause trouble due to downloading limitations issued by Google. As an alternative approach, one can now download datasets using another host (server hosted by the University of Oslo), through the argument googledrive = FALSE in oncoEnrichR::load_db()
• Protein-protein interactions
  • Users can opt to show isolated nodes (nodes with no interactions) or not - logical argument to onco_enrich(): ppi_show_isolated_nodes (default FALSE)
  • Added protein-protein interaction network based on interactions found in BioGRID
    • Users can set a minimum required threshold for the number of evidence items required for each interaction in BioGRID
    • New numerical argument to onco_enrich(): ppi_biogrid_min_evidence
  • Users can restrict the STRING network to physical interactions only or an extended network also including indirect ( functional ) interactions - API network type
    • New character argument to onco_enrich(): ppi_string_network_type (physical or functional)
  • Previous argument ppi_score_threshold is now named ppi_string_min_score, with a scale that goes from 0 to 1 (as opposed to 0-1000 in previous versions)
• Subcellular compartment annotations
  • Now using the regularly updated COMPARTMENTS resource as the underlying source for annotation
  • Users can set a minimum confidence score for each target compartment annotation (range from 3 (least confident) to 5 (most confident)), as well as the required minimum number of channels ( Knowledge, Text mining or Experimental) that should support a given target compartment annotation
    • New arguments to onco_enrich(): subcellcomp_min_confidence, subcellcomp_min_channels
• Annotation of oncogenic/tumor suppressive roles
  • A revised approach to assign roles as proto-oncogenes or tumor suppressors is implemented, in which we assign each role with a confidence level (Moderate/Strong/Very strong) pending upon support in manually curated resources (Network of Cancer Genes (NCG) or Cancer Gene Census (CGC)) or support in the biomedical literature (CancerMine)

• Cancer driver annotation

  • A more conservative approach for driver gene status is implemented: requiring support from at least two distinct resources (Network of Cancer Genes (NCG), Cancer Gene Census, TCGA, IntOGen, or CancerMine)

• Argument renaming - Renamed arguments to onco_enrich() for improved naming consistency:

  • ppi_string_min_score
  • ppi_string_network_type
  • ppi_biogrid_min_evidence
  • ppi_show_drugs
  • ppi_show_isolated_nodes
  • regulatory_min_confidence
  • enrichment_p_value_cutoff
  • enrichment_q_value_cutoff
  • enrichment_p_value_adj
  • enrichment_plot_num_terms
  • enrichment_simplify_go
  • enrichment_max_geneset_size
  • enrichment_min_geneset_size
  • subcellcomp_min_confidence
  • subcellcomp_show_cytosol
  • subcellcomp_min_channels
• Other
  • added oncoEnrichR favicon to output HTML reports

Version 1.3.2

• Date: 2022-09-27

Changed

• Cancer driver classification in Cancer associations section. Driver classification is based on the union of IntOGen mutational driver catalogue (v2020-02-01) and Network of Cancer Genes (canonical drivers, v7.0)

Version 1.3.1

• Date: 2022-09-23

Added

• Data updates:
• CancerMine (20220920 - v48)
• TCGA (20220727 - v34.0)
• WikiPathways (20220910)

• Upgraded sigven/oncoPhenoMap to v0.4.0:

  • Experimental Factor Ontology (v3.46.0)
  • Human Disease Ontology (2022-08-29)

• Recurrent somatic variants (SNVs/InDels, as found in TCGA) are appended to Excel output worksheet, tab RECURRENT_VARIANTS

Fixed

• A few erroneous mutation hotspots in Tumor aberration frequencies section

Changed

• Slight modification to column names in Drug associations section
• Added links to ENSEMBL_GENE_ID in Tumor aberration frequencies section

Version 1.3.0

• Date: 2022-09-12

Added

• Data updates:
• MSigDB (August 2022.1)

Changed

• Fixed some artefacts (-AS1 entries) in the output of CancerMine
• Added approved_drugs as a column to the Drug associations section of the output report

Version 1.2.2

• Date: 2022-09-02

Added

• Data updates:
• WikiPathways (20220810)
• KEGG (20220809)

Changed

• Now using googledrive as data repository host, due to unstable code using Zenodo

Version 1.2.1

• Date: 2022-07-13

Added

• Data updates:
• WikiPathways (20220610)
• Open Targets Platform (2022.06)
• CancerMine (v47)

Version 1.2.0

• Date: 2022-06-24

Changed

• Moved to zenodo.org for hosting underlying datasets, accessed with zen4R
• MAF objects (TCGA) no longer loaded from GitHub
• Function oncoEnrichR::write() now requires the oncoEnrichR database object (oeDB) as an argument

Version 1.1.1

• Date: 2022-06-16

Added

• Data updates:
• WikiPathways (20220610)
• Configurations for onco_enrich() populated at the end of HTML report

Changed

• Option renaming
• show_prognostic_cancer_assoc renamed to show_prognostic.
• show_tcga_aberration renamed to show_aberration
• show_regulatory_interactions renamed to show_regulatory
• show_tcga_coexpression renamed to show_coexpression

Fixed

• Bug: database loading missing pfamdb
• Relaxed dependency versions (caused conflicts for R versions < 4.2)

Version 1.1.0

• Date: 2022-06-10

Added

• Data updates:
• CancerMine (v46)
• Open Targets Platform (2022.04)
• WikiPathways (20220510)
• GENCODE (v40)
• CGC (v96)
• TCGA (GDC release 32)

• EFO (v42.0)

• Module that shows the occurrence of protein domains among query set members

• Protein-complex cancer relevance score
• New options
• ppi_node_shadow - logical indicating if nodes in the PPI network should carry a shadow or not
• show_domain - logical indicating if report should add section on protein domain frequencies in query set

Changed

• Re-ordering of HTML sections, multiple cosmetic changes
• GO enrichment plots: now showing q-value and enrichment factors in bar plots
• Revised method to compute tumor-type specific cancer rank (and global)
• Dedicated output article with output views on sigven.github.io/oncoEnrichR

Fixed

• Bug: duplicate records in retrieved co-expression pairs
• Removed most redundant protein complexes in OmniPath

Version 1.0.9

• Date: 2022-03-31

Added

• Data updates:
• CancerMine (v43)
• Open Targets Platform (2022.02)
• WikiPathways (20220310)

• Project Score (July 2021 release)

• New analysis section: Synthetic lethality - shows how members of the queryset overlaps with predicted synthetic lethality interactions (as published by De Kegel et al., Cell Systems, 2021)

• add this section in the output with option --show_synleth

Fixed

• Bug in query identification for background set
• Bug in rank of top gene-cancer associations

Changed

• Option --show_crispr_lof renamed to --show_fitness. Corresponding section in HTML report renamed from CRISPR/Cas9 loss-of-fitness to Gene fitness scores.
• Renamed sections in HTML report:
• TCGA co-expression --> Tumor co-expression
• TCGA aberration frequency ---> Tumor aberration frequencies

• TCGA prognostic associations ---> Prognostic associations

• Sections that include tabsets are now organized so that the initial active tab always contains data (with the exception of all tabs being empty)

Version 1.0.8

• Date: 2022-02-18

Added

• Data updates:
• WikiPathways (20220210)
• CancerMine (v42)
• MSigDB (v7.5.1)
• GENCODE (v39)
• Gene summary (NCBI)
• Reactome/GO (MSigDB v7.5.1)
• KEGG (20211223)

Changed

• Refactoring of code and data for mapping gene identifiers
• Refactoring of code for database loading

Version 1.0.7

• Date: 2021-11-30

Added

• Data updates
• WikiPathways (20211110)
• Open Targets Platform (2021.11)
• EFO (v3.36.0)
• TCGA (v31, 2021-10-29)
• CancerMine (v40)
• Human Protein Atlas (v21)
• UniProt KB (2021_04)
• PFAM domains (release 35, November 2021)

Changed

• Management of annotation databases have been re-designed, reducing the size and installation of oncoEnrichR significantly. The re-design results in the addition of an initial step in the analysis; database loading.

Version 1.0.6

• Date: 2021-10-27

Added

• Data updates
• KEGG (20211013)
• WikiPathways (20211010)
• Open Targets Platform (2021.09)
• EFO (v3.35.0), DiseaseOntology (v2021-10-11)
• TCGA (v30, 2021-09-23)

• Protein complex annotations - additions from Compleat, ComplexPortal, PDB, hu.MAP2

• New functionality

• Report modules

  • Regulatory interactions - (DoRothEA)
    • View overlap between members of queryset with previously established regulatory interactions (TF-target relationships) from the DoRothEA resource
  • Ligand-receptor interactions - (CellChatDB)
    • Explore potential ligand-receptor interactions in the query set, as found in the CellChat database

• Report styling options

  • Choose your own Bootswatch theme for HTML report - option html_report_theme
  • Choose where the table of contents are placed in the HTML report (floating-left or static at the top) - option html_floating_toc

• Arguments to oncoEnichR::onco_enrich():

  • html_floating_toc - logical, if set to FALSE, table of contents in HTML report will be placed on top of the main document
  • html_report_theme - character, choose between different Bootswatch themes for style in HTML report
  • show_regulatory - logical, show regulatory interactions module (DoRothEA)
  • min_confidence_reg_interaction - character, minimum confidence of regulatory interactions included from DoRothEA ('A','B','C', or 'D')
  • show_ligand_receptor - logical, show ligand-receptor interaction module (CellChatDB)
  • num_terms_enrichment_plot - integer, number of enriched Gene Ontology terms (max) to show in enrichment barplots (module Functional Enrichment)

• Default gene rankings

  • In the modules Regulatory Interactions and Tissue and cell type enrichment, interactions/targets are ranked according to a quantitative cancer association score cancer_max_rank (maximum gene-cancer association rank (Open Targets Platform) across primary sites)

Fixed

• Report disclaimer occurring at the bottom of the report is no longer missing from web-based analysis (oncotools.elixir.no) - file _site.yml in inst/templates

sigven/oncoEnrichR documentation built on Aug. 31, 2023, 8:05 a.m.