19 Reference
19.1 Data source
Below is a list of public database used in myCMIE app:
| Data type | Platform | Source |
|---|---|---|
| Clinical studies | Clinicaltrial.gov | link |
| Mutation/Copy number/RNA-seq/RPPA | TCGA/Xena UCSC | link |
| Mutation/Copy number/RNA-seq/RPPA | CCLE/Xena UCSC | link |
| Hallmark gene sets | MSigDB | link |
| Human DNA Repair Genes | MDACC | link |
| IC50 for cell lines (Drug sensitivity) | GDSC | link |
| Methylation-based CIBERSORT | A. Chakravarthy et al. (2018) | link |
| Expression-based CIBERSORT | GDC | link |
| Census Genes Mutations (GRCh37, Release v98) | COSMIC | link |
| TMB and Immunotherapy (MSK, Nat Genet 2019) | Samstein et al. (2019) | PMID: 30643254 |
| METABRIC, Nature 2012 & Nat Commun 2016 |
Pereira et al. (2016) Curtis et al. (2012) |
PMID: 27161491 PMID: 22522925 |
| NCI Patient-Derived Models Repository (PDMR) | Frederick National Laboratory for Cancer Research | https://pdmr.cancer.gov/. |
| PDX-PanCanAtlas | Sun et al. (2021) | PMID: 34429404 |
| PDX (Breast cancer) | Baylor Medical College | Personal Communication |
| cBioPortal | Bruijn et al. (2023) | https://www.cbioportal.org/ |
| NBBC (Non-B DNA Burden in Cancer) | Xu and Kowalski, 2023 | PMID: 37224529 |
19.2
Anand, Lakshay, and Carlos M. Rodriguez Lopez. 2022. “ChromoMap: An R Package for Interactive Visualization of Multi-Omics Data and Annotation of Chromosomes.” BMC Bioinformatics 23 (1). https://doi.org/10.1186/s12859-021-04556-z.
Chakravarthy, Ankur, Andrew Furness, Kroopa Joshi, Ehsan Ghorani, Kirsty Ford, Matthew J. Ward, Emma V. King, et al. 2018. “Pan-Cancer Deconvolution of Tumour Composition Using DNA Methylation.” Nature Communications 9 (1). https://doi.org/10.1038/s41467-018-05570-1.
Chao, Eva, Qi Xu, Anna Capasso, S. Gail Eckhardt, and Jeanne Kowalski. 2021. “Differential Gain of Chromosomal Regions 20q or 13q with Loss of 8p and 18q Differentiates Disease-Free Survival in Colorectal Cancer.” Journal of Clinical Oncology 39 (3_suppl): 126–26. https://doi.org/10.1200/JCO.2021.39.3\_suppl.126.
Kowalski, Jeanne, Qi Xu, Hsueh Ping Chao, Heta Gandhi, Kyaw Lwin Aung, and William H. Matsui. 2022. “KRAS Mutation Methylation Clonality in Early-Stage Pancreatic Cancer.” Journal of Clinical Oncology 40 (4_suppl): 614–14. https://doi.org/10.1200/JCO.2022.40.4\_suppl.614.
Lange, Sabine S., Kei-ichi Takata, and Richard D. Wood. 2011. “DNA Polymerases and Cancer.” Nature Reviews Cancer 11 (2): 96–110. https://doi.org/10.1038/nrc2998.
Liberzon, A., A. Subramanian, R. Pinchback, H. Thorvaldsdottir, P. Tamayo, and J. P. Mesirov. 2011. “Molecular Signatures Database (MSigDB) 3.0.” Bioinformatics 27 (12): 1739–40. https://doi.org/10.1093/bioinformatics/btr260.
Ronen, Amiram, and Barry W. Glickman. 2001. “Human DNA Repair Genes.” Environmental and Molecular Mutagenesis 37 (3): 241–83. https://doi.org/10.1002/em.1033.
Thorsson, Vésteinn, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, et al. 2018. “The Immune Landscape of Cancer.” Immunity 48 (4): 812–830.e14. https://doi.org/10.1016/j.immuni.2018.03.023.
Wu, Tianzhi, Erqiang Hu, Shuangbin Xu, Meijun Chen, Pingfan Guo, Zehan Dai, Tingze Feng, et al. 2021. “clusterProfiler 4.0: A Universal Enrichment Tool for Interpreting Omics Data.” The Innovation 2 (3): 100141. https://doi.org/10.1016/j.xinn.2021.100141.
Yang, Wanjuan, Jorge Soares, Patricia Greninger, Elena J. Edelman, Howard Lightfoot, Simon Forbes, Nidhi Bindal, et al. 2012. “Genomics of Drug Sensitivity in Cancer (GDSC): A Resource for Therapeutic Biomarker Discovery in Cancer Cells.” Nucleic Acids Research 41 (D1): D955–61. https://doi.org/10.1093/nar/gks1111.