Document
1. Datasets
The datasets used in this study come from the Genomics of Drug Sensitivity in Cancer (GDSC)[1]. These datasets can be downloaded from the following link:
Dataset: GDSC portal
2. Tools
In this study, various tools were used for feature extraction and analysis, including pubchem[2], DESeq2[3], TIMER[4], and HPAanalyze[5]. Detailed instructions for installation and configuration are provided in the following links:
pubchempy: https://pubchem.ncbi.nlm.nih.gov/
DESeq2: https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
TIMER: https://cistrome.shinyapps.io/timer/
HPAanalyze: https://www.bioconductor.org/packages/release/bioc/html/HPAanalyze.html
3. References
[1] Iorio, Francesco, Theo A. Knijnenburg, Daniel J. Vis, Graham R. Bignell, Michael P. Menden, Michael Schubert, Nanne Aben et al. "A landscape of pharmacogenomic interactions in cancer." Cell 166, no. 3 (2016): 740-754. [2] Kim, Sunghwan, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li et al. "PubChem 2019 update: improved access to chemical data." Nucleic acids research 47, no. D1 (2019): D1102-D1109. [3] Love, Michael I., Wolfgang Huber, and Simon Anders. "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome biology 15 (2014): 1-21. [4] Li, Taiwen, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, and X. Shirley Liu. "TIMER2. 0 for analysis of tumor-infiltrating immune cells." Nucleic acids research 48, no. W1 (2020): W509-W514. [5] Tran, Anh Nhat, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, and Anita B. Hjelmeland. "HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data." Bmc Bioinformatics 20 (2019): 1-11.