Identification of common key genes in breast, lung and prostate cancer and exploration of their heterogeneous expression
- Richa K. Makhijani
- Shital A. Raut
- Hemant J. Purohit
Published online on: November 30, 2017
Copyright: © Makhijani et al.
This is an open access article distributed under the terms of Creative Commons Attribution License.
Cancer is one of the leading causes of mortality worldwide, and in particular, breast cancer in women, prostate cancer in men, and lung cancer in both women and men. The present study aimed to identify a common set of genes which may serve as indicators of important molecular and cellular processes in breast, prostate and lung cancer. Six microarray gene expression profile datasets [GSE45827, GSE48984, GSE19804, GSE10072, GSE55945 and GSE26910 (two datasets for each cancer)] and one RNA‑Seq expression dataset (GSE62944 including all three cancer types), were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in each individual cancer type using the LIMMA statistical package in R, and then a comparison of the resulting gene lists was performed to identify common DEGs across cancer types. This analysis was performed for microarray and RNA‑Seq datasets individually, revealing a set of 62 and 1,290 differentially expressed genes respectively, which may be associated with the three cancers. Out of these genes, 44 were common to both analyses, and hence termed key genes. Gene Ontology functional annotation, Kyoto Encyclopedia of Genes and Genomes pathway mapping and literature citations were used to confirm the role of the key genes in cancer. Finally, the heterogeneity of expression of the key genes was explored using the I2 statistic (meta package in R). The results demonstrated non‑heterogeneous expression of 6 out of the 44 key genes, whereas the remaining genes exhibited significant heterogeneity in expression across microarray samples. In conclusion, the identified DEGs may play important roles in the pathogenesis of breast, prostate and lung cancer and may be used as biomarkers for the development of novel diagnostic and therapeutic strategies.