Identification of potential biomarkers for pancreatic ductal adenocarcinoma: a bioinformatics analysis

Abstract

PDA is an aggressive cancer with a 5-year survival rate, which is very low. There is no effective prognosis or therapy for PDA because of the lack of target biomarkers. The objective of this article is to identify the target biomarkers for PDA using a bioinformatics approach. In this work, we have analysed the three microarray datasets from the NCBI GEO database. We used the Geo2R tool to analyse the microarray data with the Benjamini and Hochberg false discovery rate method, and the significance level cut-off was set to 0.05. We have identified 659 DEGs from the datasets. There are a total of 15 hub genes that were selected from the PPI network constructed using the STRING application. Furthermore, these 15 genes were evaluated on PDA patients using TCGA and GTEx databases in (GEPIA). The online tool DAVID was used to analyse the functional annotation information for the DEGs. The functional pathway enrichment was performed on the GO and KEGG. The hub genes were mainly enriched for cell division, chromosome segregation, protein binding and microtubule binding. Further, the gene alteration study was performed using the cBioportal tool and screened out six hub genes (ASPM, CENPF, BIRC5, TTK, DLGAP5, and TOP2A) with a high alteration rate in PDA samples. Furthermore, Kaplan–Meier survival analysis was performed on the six hub genes and identified poor-survival outcomes that may be involved in tumorigenesis and PDA development. So, this study concludes that, these six hub genes may be potential prognostic biomarkers for PDA.

Keywords:

• Cancer
• PDA
• bioinformatics
• biomarkers
• DEGs
• hub genes

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The following information was supplied regarding data availability:

Three microarray datasets are available at NCBI GEO: GSE41372, GSE16515, GSE71989. https://www.ncbi.nlm.nih.gov/geo/

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.