CancerDrugsDB - no genes names

[saezlab]

CancerDrugsDB - no genes names

[deeenes]

Hello,

CancerDrugsDB in the OmniPath Annotations database provides annotations for about 200 drug compounds:

library(OmnipathR)
cddb <- import_omnipath_annotations(resource = 'CancerDrugsDB', wide = TRUE)                                                              
[2023-01-10 18:06:58] [SUCCESS] [OmnipathR] Downloaded 1554 annotation records.
cddb
# A tibble: 195 × 11
    uniprot genesymbol    entity_type    drug_label    ema_approved fda_approved european_national_approved who_approved generic approval_…¹ indic…²
      <dbl> <chr>         <chr>          <chr>         <lgl>        <lgl>        <lgl>                      <lgl>        <lgl>         <dbl> <chr>  
 1 46220502 VERZENIO      small_molecule Abemaciclib   TRUE         TRUE         FALSE                      FALSE        FALSE          2017 Advanc…
 2   132971 ABIRATERONE   small_molecule Abiraterone   TRUE         TRUE         FALSE                      TRUE         TRUE           2011 Metast…
 3 71226662 ACALABRUTINIB small_molecule Acalabrutinib TRUE         TRUE         FALSE                      FALSE        FALSE          2017 Chroni…
 4   451415 ACLARUBICIN   small_molecule Aclarubicin   FALSE        FALSE        FALSE                      FALSE        FALSE            NA NA     
 5 86289437 ACLARUBICIN   small_molecule Aclarubicin   FALSE        FALSE        FALSE                      FALSE        FALSE            NA NA     
 6 10184653 GILOTRIF      small_molecule Afatinib      TRUE         TRUE         FALSE                      FALSE        FALSE          2013 Metast…
 7 49806720 ALECENSA      small_molecule Alectinib     TRUE         TRUE         FALSE                      FALSE        FALSE          2015 Refrac…
 8   449171 ALITRETINOIN  small_molecule Alitretinoin  TRUE         TRUE         FALSE                      FALSE        FALSE          1999 NA     
 9 56649450 ALPELISIB     small_molecule Alpelisib     TRUE         TRUE         FALSE                      FALSE        FALSE          2019 Advanc…
10     2123 HEXALEN       small_molecule Altretamine   FALSE        FALSE        TRUE                       FALSE        FALSE          1990 Ovaria…
# … with 185 more rows, and abbreviated variable names ¹​approval_year, ²​indications
# ℹ Use `print(n = ...)` to see more rows

The columns are called uniprot and genesymbol only for historical reasons. In fact, for drugs we use PubChem CIDs as default identifier, hence you find these in the uniprot column; and in the genesymbol column we show the rxnorm names, as these are typically human readable labels.

If you are interested in the canonical targets from CancerDrugsDB, you can find those by the interactions query. As targets are genes or proteins, they have UniProt IDs and gene symbols.

cddb_targets <- import_omnipath_interactions(resources = 'CancerDrugsDB', datasets = 'small_molecule')                                    
[2023-01-10 18:11:53] [SUCCESS] [OmnipathR] Downloaded 1683 interactions.
[ins] r$> cddb_targets                                                                                                                              
# A tibble: 1,683 × 15
     source target source_genesymbol target_genesymbol is_directed is_stim…¹ is_in…² conse…³ conse…⁴ conse…⁵ sources refer…⁶ curat…⁷ n_ref…⁸ n_res…⁹
      <dbl> <chr>  <chr>             <chr>                   <dbl>     <dbl>   <dbl>   <dbl>   <dbl>   <dbl> <chr>   <chr>     <dbl>   <dbl>   <int>
 1 71481097 O14980 SELINEXOR         XPO1                        1         0       1       1       0       1 Cancer… SIGNOR…       1       1       2
 2   451668 P26358 DACOGEN           DNMT1                       1         0       1       1       0       1 Cancer… SIGNOR…       1       1       2
 3     9444 P26358 VIDAZA            DNMT1                       1         0       1       1       0       1 Cancer… SIGNOR…       1       1       2
 4   449171 P10276 ALITRETINOIN      RARA                        1         1       0       1       1       0 Cancer… SIGNOR…       1       1       2
 5   449171 P10826 ALITRETINOIN      RARB                        1         1       0       1       1       0 Cancer… SIGNOR…       1       1       2
 6   449171 P13631 ALITRETINOIN      RARG                        1         1       0       1       1       0 Cancer… SIGNOR…       1       1       2
 7   449171 P19793 ALITRETINOIN      RXRA                        1         1       0       1       1       0 Cancer… SIGNOR…       1       1       2
 8 10184653 P00533 GILOTRIF          EGFR                        1         0       1       1       0       1 Cancer… SIGNOR…       2       2       2
 9 10184653 P04626 GILOTRIF          ERBB2                       1         0       1       1       0       1 Cancer… SIGNOR…       2       2       2
10 10184653 Q15303 GILOTRIF          ERBB4                       1         0       1       1       0       1 Cancer… SIGNOR…       1       1       2
# … with 1,673 more rows, and abbreviated variable names ¹​is_stimulation, ²​is_inhibition, ³​consensus_direction, ⁴​consensus_stimulation,
#   ⁵​consensus_inhibition, ⁶​references, ⁷​curation_effort, ⁸​n_references, ⁹​n_resources
# ℹ Use `print(n = ...)` to see more rows

Best,

Denes