Abstract
As breast cancer is a multistage progression disease resulting from a genetic sequence of mutations, understanding the genes whose expression values increase or decrease monotonically across pathologic stages can provide insightful clues about how breast cancer initiates and advances. Utilizing variational autoencoder (VAE) networks in conjunction with traditional statistical testing, we successfully ascertain long non-coding RNAs (lncRNAs) that exhibit monotonically differential expression values in breast cancer. Subsequently, we validate that the identified lncRNAs really present monotonically changed patterns. The proposed procedure identified 248 monotonically decreasing expressed and 115 increasing expressed lncRNAs. They correspond to a total of 65 and 33 genes respectively, which possess unique known gene symbols. Some of them are associated with breast cancer, as suggested by previous studies. Furthermore, enriched pathways by the target mRNAs of these identified lncRNAs include the Wnt signaling pathway, human papillomavirus (HPV) infection, and Rap 1 signaling pathway, which have been shown to play crucial roles in the initiation and development of breast cancer. Additionally, we trained a VAE model using the entire dataset. To assess the effectiveness of the identified lncRNAs, a microarray dataset was employed as the test set. The results obtained from this evaluation were deemed satisfactory. In conclusion, further experimental validation of these lncRNAs with a large-sized study is warranted, and the proposed procedure is highly recommended.
Document Type
Article
Publication Date
8-2023
Digital Object Identifier (DOI)
https://doi.org/10.1371/journal.pone.0289971
Funding Information
This study was supported by a fund (JJKH20190032KJ) from the Education Department of Jilin Province. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Repository Citation
Wang, Dongjiao; Gao, Ling; Gao, Xinliang; Wang, Chi; and Tian, Suyan, "Identification of monotonically expressed long non-coding RNA signatures for breast cancer using variational autoencoders" (2023). Markey Cancer Center Faculty Publications. 342.
https://uknowledge.uky.edu/markey_facpub/342
Notes/Citation Information
© 2023 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.