@article{04a178fb93254d6bbca38e9473122f37,
title = "Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics",
abstract = "A major manifestation of cancer is the alteration of protein measurements. However, proteins are harder and more expensive to measure than genes and transcripts. To address this problem, we crowdsourced it via the NCI-CPTAC DREAM proteogenomics challenge. We provided participants data to build models to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. We then asked participants to use such models to predict unseen (phospho)protein data from given genomic and transcriptomic data in other patients. This experiment allowed us to assess the predictive performance of the proposed methods in an unbiased and “double-blinded” manner. We found that ensemble methods perform better, and we identified which proteins and biological processes are easier or harder to predict. In general, performance was limited, suggesting that (phospho)proteomic cannot be replaced, at least yet, by genomic and transcriptomic profiling.",
keywords = "cancer, crowdsourcing, genomics, machine learning, protein regulation, proteogenomics, proteomics",
author = "{NCI-CPTAC-DREAM Consortium} and Mi Yang and Francesca Petralia and Zhi Li and Hongyang Li and Weiping Ma and Xiaoyu Song and Sunkyu Kim and Heewon Lee and Han Yu and Bora Lee and Seohui Bae and Eunji Heo and Jan Kaczmarczyk and Piotr St{\c e}pniak and Micha{\l} Warcho{\l} and Thomas Yu and Calinawan, {Anna P.} and Boutros, {Paul C.} and Payne, {Samuel H.} and Boris Reva and Tunde Aderinwale and Ebrahim Afyounian and Piyush Agrawal and Mehreen Ali and Alicia Amadoz and Francisco Azuaje and John Bachman and Sherry Bhalla and Jos{\'e} Carbonell-Caballero and Priyanka Chakraborty and Kumardeep Chaudhary and Yonghwa Choi and Yoonjung Choi and Cankut {\c C}ubuk and Dhanda, {Sandeep Kumar} and Joaqu{\'i}n Dopazo and Elo, {Laura L.} and {\'A}bel F{\'o}thi and Olivier Gevaert and Kirsi Granberg and Russell Greiner and Hidalgo, {Marta R.} and Vivek Jayaswal and Hwisang Jeon and Minji Jeon and Kalmady, {Sunil V.} and Yasuhiro Kambara and Jaewoo Kang and Keunsoo Kang and Pei Wang",
note = "Publisher Copyright: {\textcopyright} 2020 The Authors",
year = "2020",
month = aug,
day = "26",
doi = "10.1016/j.cels.2020.06.013",
language = "English",
volume = "11",
pages = "186--195.e9",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Cell Press",
number = "2",
}