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Breast Cancer Case Identification Based on Deep Learning and Bioinformatics Analysis - 2021

Breast Cancer Case Identification Based On Deep Learning And Bioinformatics Analysis

Research Paper on Breast Cancer Case Identification Based On Deep Learning And Bioinformatics Analysis

Research Area:  Machine Learning

Abstract:

Mastering the molecular mechanism of breast cancer (BC) can provide an in-depth understanding of BC pathology. This study explored existing technologies for diagnosing BC, such as mammography, ultrasound, magnetic resonance imaging (MRI), computed tomography (CT), and positron emission tomography (PET) and summarized the disadvantages of the existing cancer diagnosis. The purpose of this article is to use gene expression profiles of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to classify BC samples and normal samples. The method proposed in this article triumphs over some of the shortcomings of traditional diagnostic methods and can conduct BC diagnosis more rapidly with high sensitivity and have no radiation. This study first selected the genes most relevant to cancer through weighted gene co-expression network analysis (WGCNA) and differential expression analysis (DEA). Then it used the protein–protein interaction (PPI) network to screen 23 hub genes. Finally, it used the support vector machine (SVM), decision tree (DT), Bayesian network (BN), artificial neural network (ANN), convolutional neural network CNN-LeNet and CNN-AlexNet to process the expression levels of 23 hub genes. For gene expression profiles, the ANN model has the best performance in the classification of cancer samples. The ten-time average accuracy is 97.36% (±0.34%), the F1 value is 0.8535 (±0.0260), the sensitivity is 98.32% (±0.32%), the specificity is 89.59% (±3.53%) and the AUC is 0.99. In summary, this method effectively classifies cancer samples and normal samples and provides reasonable new ideas for the early diagnosis of cancer in the future.

Keywords:  
Breast Cancer
Deep Learning
Bioinformatics Analysis
positron emission tomography
magnetic resonance imaging (MRI)
computed tomography

Author(s) Name:  Dongfang Jia, Cheng Chen, Chen Chen, Fangfang Chen, Ningrui Zhang, Ziwei Yan and Xiaoyi Lv

Journal name:  Frontiers in Genetics

Conferrence name:  

Publisher name:  Frontiers Media S.A.

DOI:  10.3389/fgene.2021.628136

Volume Information: