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. 2022 Feb 15:13:856075.
doi: 10.3389/fgene.2022.856075. eCollection 2022.

Analysis of Breast Cancer Based on the Dysregulated Network

Affiliations

Analysis of Breast Cancer Based on the Dysregulated Network

Yanhao Huo et al. Front Genet. .

Abstract

Breast cancer is a heterogeneous disease, and its development is closely associated with the underlying molecular regulatory network. In this paper, we propose a new way to measure the regulation strength between genes based on their expression values, and construct the dysregulated networks (DNs) for the four subtypes of breast cancer. Our results show that the key dysregulated networks (KDNs) are significantly enriched in critical breast cancer-related pathways and driver genes; closely related to drug targets; and have significant differences in survival analysis. Moreover, the key dysregulated genes could serve as potential driver genes, drug targets, and prognostic markers for each breast cancer subtype. Therefore, the KDN is expected to be an effective and novel way to understand the mechanisms of breast cancer.

Keywords: breast cancer; cancer-related pathways; driver genes; drug targets; dysregulated network; survival analysis.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Overview of the analysis workflow.
FIGURE 2
FIGURE 2
The dysregulated network (DN) of breast cancer. (A) The heatmap of the dysregulated interactions in the four breast cancer subtypes. (B) The percentage of interactions with 0, 1, and 2 DEGs (gray color) and dysregulated interactions (red color) in the background influence network. (C) The scatter plot of the dysregulation score and out-degree of genes in the DN. (D) The relationship between the cumulative dysregulation score and the number of genes in the DN.
FIGURE 3
FIGURE 3
The relation of the top 20 key genes and their enriched pathways.
FIGURE 4
FIGURE 4
Driver gene analysis. (A) Venn diagrams of the key genes and driver genes. (B) The average number of events of key driver genes and other driver genes. (C) KDN with driver genes in green color.
FIGURE 5
FIGURE 5
Drug target analysis. (A) The Venn graph of the targets of 29 breast cancer drugs and genes in the KDN. (B) The enrichment scores of 29 breast cancer targeted drugs.
FIGURE 6
FIGURE 6
Survival analysis (Kaplan-Meier plots) of dysregulated biomarkers. biomarkers High values are shown in red and low values are shown in black.

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