An operational perturbation proteomics-based virtual cell model - Nature

Data availability

Raw mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium available via iProX (IPX0007409000). The PTDS protein matrix and associated resources are available for academic and non-commercial use through the open-access platform db.prottalks.com. Other data used are available from the Kyoto Encyclopedia of Genes and Genomes pathway at https://www.genome.jp/kegg/pathway.html (ref. 57), from Metascape at https://metascape.org/gp/ (ref. 58), from STRING at https://cn.string-db.org/ (ref. 59) and from Ingenuity Pathway Analysis at http://www.ingenuity.com (ref. 60).

Code availability

The project data analysis codes are available via GitHub at https://github.com/guomics-lab/PTV-1.

ReferencesBunne, C. et al. How to build the virtual cell with artificial intelligence: priorities and opportunities. Cell 187, 7045–7063 (2024).Article