| Deposited data |
|
| cBioPortal |
Cerami et al. (2012); Gao et al. (2013)
|
https://www.cbioportal.org/; RRID:SCR_014555
|
| Cancer Dependency Map (DepMap) 20Q4 |
Ghandi et al. (2019) |
https://depmap.org/portal/ccle/; https://figshare.com/articles/dataset/DepMap_20Q4_Public/13237076; RRID:SCR_017655
|
| LinkedOmics |
Vasaikar et al. (2018) |
http://www.linkedomics.org/ |
| CPTAC Python API |
Lindgren et al. (2021) |
https://pypi.org/project/cptac/ |
| CORUM 3.0 |
Giurgiu et al. (2019) |
http://mips.helmholtz-muenchen.de/corum/; RRID:SCR_002254
|
| KEGG Pathway |
Kanehisa (2019); Kanehisa and Goto (2000); Kanehisa et al. (2021)
|
https://www.genome.jp/kegg/pathway.html; RRID:SCR_018145
|
| Colorectal cancer transcriptomics |
Cancer Genome Atlas Network (2012) |
https://cbioportal-datahub.s3.amazonaws.com/coadread_tcga_pub.tar.gz |
| Colorectal cancer proteomics |
Zhang et al. (2014) |
Published supplemental Table S4 |
| Ovarian cancer transcriptomics |
Cancer Genome Atlas Research Network (2011) |
http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/OV/20160128/gdac.broadinstitute.org_OV.mRNA_Preprocess_Median.Level_3.2016012800.0.0.tar.gz |
| Ovarian cancer proteomics |
Zhang et al. (2016) |
Published supplemental Table S2 |
| Breast Cancer (2016) transcriptomics |
Ciriello et al. (2015) |
https://cbioportal-datahub.s3.amazonaws.com/brca_tcga_pub2015.tar.gz |
| Breast Cancer (2016) proteomics |
Mertins et al. (2016) |
Published supplemental Table S3 |
| Colon Cancer |
Vasaikar et al. (2019) |
http://linkedomics.org/cptac-colon/ |
| Clear cell renal carcinoma |
Clark et al. (2019) |
https://pypi.org/project/cptac/ |
| Breast Cancer (2020) |
Krug et al. (2020) |
https://pypi.org/project/cptac/ |
| Endometrial Cancer |
Dou et al. (2020) |
https://pypi.org/project/cptac/ |
| Lung Adenocarcinoma |
Gillette et al. (2020) |
https://pypi.org/project/cptac/ |
| Head and Neck Squamous Cell Carcinoma |
Huang et al. (2021) |
https://pypi.org/project/cptac/ |
| Glioblastoma |
Wang et al. (2021) |
https://pypi.org/project/cptac/ |
| NCI60 cancer cell lines |
Guo et al. (2019) |
Published supplemental Tables S6 and S1 |
| Cancer Cell Line Encyclopedia (CCLE) transcriptomics |
Ghandi et al. (2019) |
https://depmap.org/portal/ccle/; RRID:SCR_013836
|
| CCLE proteomics |
Nusinow et al. (2020) |
Published supplemental Tables S2 and S3; https://gygi.hms.harvard.edu/publications/ccle.html
|
| GTEx healthy tissues |
Jiang et al. (2020) |
Published supplemental Tables S3 and S4 |
| RNA-seq of 675 commonly used human cancer cell lines |
Klijn et al. (2015) |
ArrayExpress: E-MTAB-2706 |
| Protein half-life |
Zecha et al. (2018) |
Published supplemental Table S3 |
| NCI CPTAC DREAM Proteogenomics challenge prediction scores of the best performing model (Team Guan) |
Yang et al. (2020) |
https://heidelberg.shinyapps.io/proteoexplorer/ |
|
| Software and algorithms |
|
| All analysis code |
This study |
https://github.com/cancergenetics/limitations_of_omics_reproducibility; https://doi.org/10.5281/zenodo.6956546
|
| Python version 3.8 |
Python Software Foundation |
https://www.python.org/; RRID:SCR_008394
|
| Pandas 1.2.5 |
McKinney (2011) |
https://pandas.pydata.org/; RRID:SCR_018214
|
| Numpy 1.20.2 |
Harris et al. (2020) |
https://numpy.org/; RRID:SCR_008633
|
| StatsModels 0.12.2 |
Seabold and Perktold (2010) |
https://www.statsmodels.org/stable/index.html; RRID:SCR_016074
|
| SciPy 1.7.1 |
Virtanen et al. (2020) |
https://www.scipy.org/; RRID:SCR_008058
|
| Matplotlib 3.3.4 |
Hunter (2007) |
https://matplotlib.org/; RRID: SCR_008624
|
| Seaborn 0.11.0 |
Waskom (2021) |
https://seaborn.pydata.org/; RRID:SCR_018132
|
