Gene co-expression network analysis reveals relationship between leukocyte fraction and genomic instability in dedifferentiated liposarcoma.

Dedifferentiated Liposarcoma (DDLPS) is one of the common subtypes of liposarcoma that is considered a highly malignant category. This study aims to investigate DDLPS through a system biology approach. The gene expression profiles and clinical traits of the DDLPS were acquired from The Cancer Genome Atlas (TCGA). The identification of co-expressed modules was conducted using the weighted gene co-expression network analysis. The immune cell-related gene function was studied by a web-based tool, TIMER, and, the survival analysis was performed at both the module and single-gene levels through Cox Regression analysis. Gene enrichment analysis was also conducted using the DAVID tool. One of the nine co-expressed DDLPS modules was significantly correlated with leukocyte fraction, hyper/hypo methylation, tumor purity, and chromosome instability (CIN). Based on the biological processes used to classify genes, the hub genes in a particular module play important roles in DNA repair, microtubule organizing clusters, mitotic checkpoint dysregulation, and cell proliferation signaling pathways. After screening the genes based on intra-module connectivity, module membership, and gene significance