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Get basic cancer-relevant gene annotations

Source: R/get_basic.R
get_basic.Rd

Downloads and returns a dataset that combines multiple human cancer gene annotations,i.e. from IntOGen, CancerMine, Network of Cancer Genes, Cancer Gene Census, NCBI, dbNSFP etc. The dataset comes as a list object, with two elements:

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a data frame with gene annotations (one record per gene)

Usage

get_basic(cache_dir = NA, force_download = FALSE)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

Value

metadata - A data frame with 10 rows and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used

  • abbreviation - abbreviation used in column names of records

records - A data frame with 108,648 rows and 65 columns:

  • entrezgene - NCBI Entrez identifier

  • symbol - primary gene symbol

  • gene_biotype - type of gene (ncRNA, protein-coding, or pseudo)

  • name - gene name

  • other_genename_designations - other gene name designations

  • hgnc_id - HGNC gene identifier

  • ncbi_function_summary - gene function summary (NCBI Gene)

  • cgc_hallmark - Annotated with cancer gene hallmarks(s) by Cancer Gene Census (CGC)

  • cgc_tier - Cancer Gene Census tier (TIER1/TIER2)

  • cgc_driver_tier1 - Logical indicating if gene is part of Cancer Gene Census - TIER1

  • cgc_driver_tier2 - Logical indicating if gene is part of Cancer Gene Census - TIER2

  • cgc_tsg - tumor suppressor gene (Cancer Gene Census)

  • cgc_oncogene - proto-oncogene (Cancer Gene Census)

  • cgc_somatic - logical indicating whether the cancer relevance of this gene relates to the soma (Cancer Gene Census)

  • cgc_phenotype_somatic - cancer phenotypes relevant for somatic mutations of this gene (Cancer Gene Census)

  • cgc_germline - logical indicating whether the cancer relevance of this gene relates to the germline (Cancer Gene Census)

  • cgc_phenotype_germline - cancer phenotypes relevant for germline mutations of this gene (Cancer Gene Census)

  • ncg_driver - canonical cancer driver gene according to Network of Cancer Genes (NCG)

  • ncg_tsg - tumor suppressor gene (NCG)

  • ncg_oncogene - proto-oncogene (NCG)

  • ncg_phenotype - cancer phenotypes relevant for this gene (NCG)

  • ncg_pmid - supporting literature identifiers (PMIDs, NCG)

  • intogen_role - cancer driver role (IntOGen)

  • intogen_phenotype - cancer phenotypes relevant for this gene (IntOGen)

  • intogen_driver - logical indicatin if gene is predicted as cancer driver by IntOGen

  • bailey2018_fp_driver - logical indicating whether this gene is likely a false positive driver gene (Bailey et al., Cell, 2018)

  • woods_dnarepair_class - class of DNA repair (DNA repair database, Woods et al.)

  • woods_dnarepair_activity - type of DNA repair activity involved (DNA repair database, Woods et al.)

  • illumina_tso500 - gene is part of Illumina's TSO500 panel (SNV_INDEL, CNA_GAIN, CNA_LOSS, RNA_FUSION)

  • foundation_one_f1cdx - gene is part of Foundation One's F1CDx panel (SNV_INDEL, CNA, FUSION, PROMOTER)

  • sanchezvega2018_signaling_pathway - curated signalling pathways (Sanchez-Vega et al., Cell, 2018)

  • cancermine_pmid_driver - PMIDs that support (from text mining) a role for this gene as a driver (CancerMine)

  • cancermine_pmid_oncogene - PMIDs that support (from text mining) a role for this gene as a proto-oncogene (CancerMine)

  • cancermine_pmid_tsg - PMIDs that support (from text mining) a role for this gene as a tumor suppressor gene (CancerMine)

  • cancermine_doid_driver - cancer phenotypes relevant for the given role (Disease Ontology identifiers, CancerMine)

  • cancermine_doid_oncogene - cancer phenotypes relevant for the given role (Disease Ontology identifiers, CancerMine)

  • cancermine_doid_tsg - cancer phenotypes relevant for the given role (Disease Ontology identifiers, CancerMine)

  • cancermine_n_cit_driver - number of citations (PMIDs) that support a role for this as a driver (CancerMine)

  • cancermine_n_cit_oncogene - number of citations (PMIDs) that support a role for this as a proto-oncogene (CancerMine)

  • cancermine_n_cit_tsg - number of citations (PMIDs) that support a role for this as a tumor suppressor (CancerMine)

  • cancermine_cit_tsg - citations for cancer driver support (all with prob > 0.8, CancerMine)

  • cancermine_cit_oncogene - citations for proto-oncogene support (all with prob > 0.8, max 50, CancerMine)

  • cancermine_cit_driver - citations for tumor suppressor gene support (all with prob > 0.8, CancerMine)

  • cancermine_cit_links_driver - citation links for cancer driver support (50 most recent, CancerMine)

  • cancermine_cit_links_oncogene - citation links for proto-oncogene support (50 most recent, CancerMine)

  • cancermine_cit_links_tsg - citation links for tumor suppressor gene support (50 most recent, CancerMine)

  • mim_id - MIM gene id (from HGNC)

  • mim_phenotype_id - MIM (ids) of the phenotype the gene caused or associated with (dbNSFP, from Uniprot)

  • prob_haploinsuffiency - Estimated probability of haploinsufficiency of the gene (from doi:10.1371/journal.pgen.1001154) (dbNSFP)

  • gene_indispensability_score - A probability prediction of the gene being essential. From doi:10.1371/journal.pcbi.1002886 (dbNSFP)

  • gene_indispensability_pred - Essential ("E") or loss-of-function tolerant ("N") based on gene_indispensability_score (dbNSFP)

  • essential_gene_crispr - Essential ("E") or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from doi: 10.1126/science.aac7041 (dbNSFP)

  • essential_gene_crispr2 - Essential ("E"), context-Specific essential ("S"), or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from http://dx.doi.org/10.1016/j.cell.2015.11.015 (dbNSFP)

  • prob_gnomad_lof_intolerant - the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants) based on gnomAD 2.1 data (dbNSFP)

  • prob_gnomad_lof_intolerant_hom - the probability of being intolerant of homozygous, but not heterozygous lof variants based on gnomAD 2.1 data (dbNSFP)

  • prob_gnomad_lof_tolerant_null - the probability of being tolerant of both heterozygous and homozygous lof variants based on gnomAD 2.1 data (dbNSFP)

  • prob_exac_lof_intolerant - the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants) based on ExAC r0.3 data (dbNSFP)

  • prob_exac_lof_intolerant_hom - the probability of being intolerant of homozygous, but not heterozygous lof variants based on ExAC r0.3 data (dbNSFP)

  • prob_exac_lof_tolerant_null - the probability of being tolerant of both heterozygous and homozygous lof variants based on ExAC r0.3 data (dbNSFP)

  • prob_exac_nontcga_lof_intolerant - the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants) based on ExAC r0.3 nonTCGA subset (dbNSFP)

  • prob_exac_nontcga_lof_intolerant_hom - the probability of being intolerant of homozygous, but not heterozygous lof variants based on ExAC 0.3 nonTCGA subset (dbNSFP)

  • prob_exac_nontcga_lof_tolerant_null - the probability of being tolerant of both heterozygous and homozygous lof variants based on ExAC r0.3 nonTCGA subset (dbNSFP)

  • dbnsfp_function_description - gene function description (dbNSFP/UniProtKB)

Examples

if (FALSE) { # \dontrun{
library(geneOncoX)
gene_basic <- get_basic(cache_dir = tempdir())
} # }