Crosstalk analysis of pathways in breast cancer using a network model based on overlapping differentially expressed genes

Abstract

Abstract. Multiple signal transduction pathways can affect each other considerably through crosstalk. However, the presence and extent of this phenomenon have not been rigorously studied. The aim of the present study was to identify strong and normal interactions between pathways in breast cancer and determine the main pathway. Five sets of breast cancer data were downloaded from the high-throughput Gene Expression Omnibus (GEO) and analyzed to identify differentially expressed (DE) genes using the Rank Product (RankProd) method. A list of pathways with differential expression was obtained by gene set enrichment analysis (GSEA) of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DE genes that overlapped between pathways were identified and a crosstalk network diagram based on the overlap of DE genes was constructed. A total of 1,464 DE genes and 26 pathways were identified. In addition, the number of DE genes that overlapped between specific pathways were determined, and the greatest degree of overlap was between the extracellular matrix (ECM)-receptor interaction and Focal adhesion pathways, which had 22 overlapping DE genes. Weighted pathway analysis of the crosstalk between pathways identified that Pathways in cancer was the main pathway in breast cancer.

Up-regulation of FN1, Activation of Maturation Promoting Factor and Associated Signaling Pathway Facilitates Epithelial-Mesenchymal Transition, Inhibits Apoptosis and Elevates Proliferation Rate of Breast Cancer Cells: In Silico Analysis of Microarray Datasets

“…In total 449 DEGs were identi ed (151 up-regulated and 298 down-regulated genes) including 33 common up-regulated / down-regulated genes. The role of major pathways identi ed through KEGG analysis like 'oocyte meiosis', 'p53 signaling pathway', 'focal adhesion' and 'ECM-receptor interaction' pathways in the development of various cancers including breast has already been reported by Sun et al and Bao et al [20,21]. Similarly, the role of Rennin secretion', 'regulation of active cytoskeleton', 'ABC transporters' and 'axon guidance' pathways in breast cancer has also been suggested by Vinson et al and Baumann et al [22][23][24][25].…”

Integrative analysis of highly mutated genes in hepatitis B virus‐related hepatic carcinoma

“…Different pathways are capable of influencing each other via a phenomenon called crosstalk. Especially, it is evident that the pathways could affect each other, when there is an overlap of differentially expressed genes, which have significant changes at expression level . Therefore, identification of the interaction of different pathways based on the overlap of differentially expressed genes has important implications for the understanding of the molecular mechanisms associated with the development of HBV‐related HCC.…”

“…Especially, it is evident that the pathways could affect each other, when there is an overlap of differentially expressed genes, which have significant changes at expression level. 41,42 Therefore, identification of the interaction of different pathways based on the overlap of differentially expressed genes has important implications for the understanding of the molecular mechanisms associated with the development of HBV-related HCC. In the present study, according to the overlap of upregulated mutated genes between different pathways, the complex crosstalk networks of KEGG pathways and WIKI pathways associated with upregulated mutated genes were structured ( Figure 4F).…”

A Novel Method for Pathway Identification Based on Attractor and Crosstalk in Polyarticular Juvenile Idiopathic Arthritis

“…From the screening of 12 attractors, two pathways matched the conditions: p53 and NAFLD pathways. The p53 signaling pathway (KEGG ID: 04115) is important in many diseases [28], in which p53 activation is induced by DNA damage, oxidative stress, and activated oncogenes [29]. The NAFLD (KEGG ID: 04932) has been identified as a significant pathway of pJIA.…”