Integrated analysis of RNA binding proteins in human colorectal cancer

Abstract Background: Though RNA-binding proteins play an essential role in a variety of different tumors, there is still limited effort made on the systematic analysis of RNA binding proteins (RBPs) in the survival of colorectal cancer(CRC).Methods: An analysis was conducted of the CRC transcriptome data collected from the TCGA database and RBPs were extracted from CRC. R software was applied to analyze the differentially expressed genes (DEGs) of RBPs. To identify the pathways and functional annotation of RBPs DEGs, Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were carried out using the database for annotation, visualization and integrated discovery. The interactive gene database search tool was employed to conduct protein-protein interaction analysis, while Cytoscape software was applied for visual processing. Based on the COX regression analysis of the prognostic value of interacting RBPs and survival time, the RBPs related to survival were screened out, and a prognostic model was constructed. The data stored in TCGA database was taken as the Train group, while the chip data obtained from the GEO database was treated as the Test group to verify the model. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were drawn to predict the survival period.Results: There were 314 genes up-regulated by RBPs DEGs and 155 genes down-regulated, from which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic markers were obtained.Conclusions: These twelve genes may be applicable as the predictor of CRC and play an essential role in the pathogenesis of CRC. In spite of this, it remains necessary to further explore the underlying mechanism.