ArticleScientific reports2016
A Bayesian algorithm for detecting differentially expressed proteins and its application in breast cancer research.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 6 citations in OpenAlex.
- Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion.bioRxiv : the preprint server for biology · 2025Article
- Machine learning algorithms being an auxiliary tool to predict the overall survival of patients with renal cell carcinoma using the SEER database.Translational andrology and urology · 2024Article
- Challenges and Opportunities for Bayesian Statistics in Proteomics.Journal of proteome research · 2022Review
- Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signaling and Angiogenesis.Molecular & cellular proteomics : MCP · 2017Article
- Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets.Oncotarget · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Presence of considerable noise and missing data points make analysis of mass-spectrometry (MS) based proteomic data a challenging task. The missing values in MS data are caused by the inability of MS machines to reliably detect proteins whose abundances fall below the detection limit. We developed a Bayesian algorithm that exploits this knowledge and uses missing data points as a complementary source of information to the observed protein intensities in order to find differentially expressed proteins by analysing MS based proteomic data. We compared its accuracy with many other methods using several simulated datasets. It consistently outperformed other methods. We then used it to analyse proteomic screens of a breast cancer (BC) patient cohort. It revealed large differences between the proteomic landscapes of triple negative and Luminal A, which are the most and least aggressive types of BC. Unexpectedly, majority of these differences could be attributed to the direct transcriptional activity of only seven transcription factors some of which are known to be inactive in triple negative BC. We also identified two new proteins which significantly correlated with the survival of BC patients, and therefore may have potential diagnostic/prognostic values.
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