Assessment of risk based on variant pathways and establishment of an artificial neural network model of thyroid cancer

Yinlong Zhao,
Lingzhi Zhao,
Tiezhu Mao and
Lili ZhongEmail author View ORCID ID profile

BMC Medical Genetics201920:92

https://doi.org/10.1186/s12881-019-0829-4

Received: 24 November 2018
Accepted: 17 May 2019
Published: 28 May 2019

Open Peer Review reports

Abstract

Background

This study aimed to establish an artificial neural network (ANN) model based on variant pathways to predict the risk of thyroid cancer.

Methods

The RNASeq data of 482 thyroid cancer samples were downloaded from the TCGA database. The samples were divided into low-risk and high-risk groups, followed by identification of differentially expressed genes (DEGs). Co-expression analysis and pathway enrichment analysis were then performed. The variant pathways were screened according to the functional deviation score of each pathway, and an ANN model was established. Finally, the efficiency of the ANN model for risk assessment was validated by survival analysis and analysis of an independent microarray dataset (GSE34289) for thyroid cancer.

Results

In total, 190 DEGs (85 up-regulated and 105 down-regulated) were identified between the low-risk and high-risk groups. Ten risk-related variant pathways were identified between the low-risk and high-risk groups, which were related to inflammatory and immune responses. Based on these variant pathways, an ANN model was built, consisting of an input layer, two hidden layers, and an output layer, corresponding to 15, 8, 5, and 1 neuron, respectively. Survival analysis showed that this model could effectively distinguish the samples with different risks. Analysis of microarray dataset GSE34289 showed that the accuracy of this model for predicating low-risk and high-risk samples was 77.5 and 86.0%, respectively.