Knowledge Discovery in Datasets of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer

Resell, M.; Graarud, E. P.; Rabben, H.-L.; Sharma, A.; Hagen, L.; Hoang, L.; Skogaker, N. T.; Svensson, M. K.; Amrutkar, M.; Verbeke, C. S.; Batra, S. K.; Qvigstad, G.; WANG, T. C.; Rustgi, A. K.; Chen, D.; Zhao, C.-M.

doi:10.1101/2025.02.23.639474

bioRxiv · 10.1101/2025.02.23.639474

Knowledge Discovery in Datasets of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer

Resell, M.·Graarud, E. P.·Rabben, H.-L.·Sharma, A.·Hagen, L.·Hoang, L.·Skogaker, N. T.·Svensson, M. K.·Amrutkar, M.·Verbeke, C. S.·Batra, S. K.·Qvigstad, G.·WANG, T. C.·Rustgi, A. K.·Chen, D.·Zhao, C.-M.

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Abstract

Knowledge discovery in databases (KDD) can contribute to translational research, also known as translational medicine, by bridging the gap between in vitro and in vivo studies and clinical applications. Here, we propose a systems modeling workflow for KDD. This framework includes data collection of composition model (various research models) and processing model (proteomics) and analytical model (bioinformatics, artificial intelligence/machine leaning and pattern evaluation), knowledge presentation, and feedback loops for hypothesis generation and validation. We applied this workflow to study pancreatic ductal adenocarcinoma (PDAC). Through this approach, we identified the common proteins between human PDAC and various research models in vitro (cells, spheroids and organoids) and in vivo (mouse mice). Accordingly, we hypothesized potential translational targets on hub proteins and the related signaling pathways, PDAC specific proteins and signature pathways, and high topological proteins. Thus, we suggest that this systems modeling workflow can be a valuable method for KDD, facilitating knowledge discovery in translational targets in general and in particular to PADA in this case.

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Resell, M., Graarud, E. P., Rabben, H.-L., Sharma, A., Hagen, L., Hoang, L., Skogaker, N. T., Svensson, M. K., Amrutkar, M., Verbeke, C. S., Batra, S. K., Qvigstad, G., WANG, T. C., Rustgi, A. K., Chen, D., Zhao, C.-M.. 2025-02-27. Knowledge Discovery in Datasets of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer. https://doi.org/10.1101/2025.02.23.639474

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