Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications.

ABSTRACT: We have carried out proteogenomic analysis of the breast cancer transcriptomic and proteomic data, available at The Clinical Proteomic Tumor Analysis Consortium resource, to identify novel peptides arising from alternatively spliced events as well as other noncanonical expressions. We used a pipeline that consisted of de novo transcript assembly, six frame-translated custom database, and a combination of search engines to identify novel peptides. A portfolio of 4,387 novel peptide sequences initially identified was further screened through PepQuery validation tool (Clinical Proteomic Tumor Analysis Consortium), which yielded 1,558 novel peptides. We considered the dataset of 1,558 validated through PepQuery to understand their functional and clinical significance, leaving the rest to be fu

SUBMITTER: Hari PS 

PROVIDER: S-EPMC9020135 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature