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However, the systematic analysis and integration from sequence to structure and function remains largely undeveloped. Here, as a solution, we built a workflow for the collection and analysis of proteomic data, transcriptomic data, and clinical outcomes for cancer-associated micropeptides using publicly available datasets from large cohorts. We initially identified 19\u00a0586 novel micropeptides by reanalyzing proteomic profile data from 3753 samples across 8 cancer types. Further quantitative analysis of these micropeptides, along with associated clinical data, identified 3065 that were dysregulated in cancer, with 370 of them showing a strong association with prognosis. Moreover, we employed a deep learning framework to construct a micropeptide-protein interaction network for further bioinformatics analysis, revealing that micropeptides are involved in multiple biological processes as bioactive molecules. Taken together, our atlas provides a benchmark for high-throughput prediction and functional exploration of micropeptides, providing new insights into their biological mechanisms in cancer. The HMPA is freely available at http:\/\/hmpa.zju.edu.cn.<\/jats:p>","DOI":"10.1093\/bib\/bbae510","type":"journal-article","created":{"date-parts":[[2024,10,16]],"date-time":"2024-10-16T22:18:12Z","timestamp":1729117092000},"source":"Crossref","is-referenced-by-count":1,"title":["HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights"],"prefix":"10.1093","volume":"25","author":[{"given":"Xinwan","family":"Su","sequence":"first","affiliation":[{"name":"MOE Laboratory of Biosystem Homeostasis and Protection , College of Life Sciences, , 866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang 310058,","place":["China"]},{"name":"Zhejiang University , College of Life Sciences, , 866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang 310058,","place":["China"]},{"name":"Cancer Center, Zhejiang University , 866 Yuhangtang Road, West Lake District, Hangzhou, Zhejiang 310058,","place":["China"]},{"name":"Key Laboratory of Cancer Prevention 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