Cell line ancestry for common cancer cell lines

Data are stored at extdata/cancer-cell-lines-ancestry.csv.gz They were accessed on November 15, 2021.

cell_line_ancestry()

Source

http://ecla.moffitt.org/

Download

References

Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res. 2019 Apr 1;79(7):1263-1273. doi: 10.1158/0008-5472.CAN-18-2747. Epub 2019 Mar 20. PMID: 30894373; PMCID: PMC6445675.

See also

Other Data resources: cdc_places(), cdc_social_vulnerability_index(), census_tract_zip_crosswalk(), rural_zips(), zipcode_shapes()

Examples

cl_ancestry = cell_line_ancestry()

head(cl_ancestry)

#>          id aliases  cvcl        ethnicity   tissue    histology
#> 1:  8-MG-BA   8MGBA _1052 African American      CNS       Glioma
#> 2:    22Rv1   22RV1 _1045                  Prostate    Carcinoma
#> 3: 42-MG-BA  42MGBA _1798                       CNS       Glioma
#> 4:      59M         _2291                     Ovary    Carcinoma
#> 5:     143B         _2270        Caucasian     Bone Osteosarcoma
#> 6:     201T         _X481                      Lung    Carcinoma
#>            subhistology age  source ccle_membership ccle_membership eur-south
#> 1: Astrocytoma Grade IV  54 Primary               Y                  0.331867
#> 2:       Adenocarcinoma  NA Primary               Y                  0.306245
#> 3: Astrocytoma Grade IV  63                       Y                  0.318954
#> 4:                       65                       Y                  0.339103
#> 5:                       13                       Y                  0.589814
#> 6:       Adenocarcinoma  NA Primary                                  0.055498
#>    native american e.asian-south e.asian-north  s.asian eur-north  african
#> 1:        0.000957      0.000010      0.025278 0.022865  0.619013 0.000010
#> 2:        0.002324      0.000010      0.005170 0.002725  0.674582 0.008944
#> 3:        0.000010      0.000010      0.048757 0.000010  0.632205 0.000054
#> 4:        0.000010      0.000010      0.041761 0.000010  0.587073 0.032033
#> 5:        0.000010      0.040158      0.000010 0.369989  0.000010 0.000010
#> 6:        0.000010      0.000010      0.025811 0.000010  0.030603 0.888057
#>                                        cvcl_url
#> 1: https://web.expasy.org/cellosaurus/CVCL_1052
#> 2: https://web.expasy.org/cellosaurus/CVCL_1045
#> 3: https://web.expasy.org/cellosaurus/CVCL_1798
#> 4: https://web.expasy.org/cellosaurus/CVCL_2291
#> 5: https://web.expasy.org/cellosaurus/CVCL_2270
#> 6: https://web.expasy.org/cellosaurus/CVCL_X481

# Source of cell line
table(cl_ancestry$source)

#> 
#>              Metastasis Metastasis      Primary   Recurrent 
#>         672         186          13         519           3 

# cell lines in CCLE?
table(cl_ancestry$ccle_membership)

#> 
#>         Y 
#>  357 1036 

table(cl_ancestry$ethnicity)

#> 
#>                                 African    African American      African, Black 
#>                 641                   9                   1                   5 
#>            American     American Indian               Asian               Black 
#>                   1                   1                  51                  25 
#>      Black, African           Caucasian Caucasian, European    Caucasian, White 
#>                   2                 415                   1                  25 
#>             Chinese            European    European, French            Hispanic 
#>                   2                   1                   1                   2 
#>              Indian            Japanese       Korean, Asian       North African 
#>                   1                 190                   7                   1 
#>    Taiwanese, Asian             Turkish               White 
#>                   1                   1                   9 

anc_mat = as.matrix(cl_ancestry[,12:18])
heatmap(anc_mat,margins = c(9,1), labRow=NA)