Makhijani Richa K, Raut Shital A, Purohit Hemant J
Department of Computer Science and Engineering, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India.
Environmental Genomics Division, National Environmental Engineering Research Institute, Nagpur, Maharashtra 440020, India.
Oncol Lett. 2018 Feb;15(2):1680-1690. doi: 10.3892/ol.2017.7508. Epub 2017 Nov 30.
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 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.
癌症是全球主要死因之一，尤其是女性乳腺癌、男性前列腺癌以及男性和女性的肺癌。本研究旨在确定一组共同的基因，这些基因可能作为乳腺癌、前列腺癌和肺癌中重要分子和细胞过程的指标。从基因表达综合数据库下载了六个微阵列基因表达谱数据集[GSE45827、GSE48984、GSE19804、GSE10072、GSE55945和GSE26910（每种癌症两个数据集）]以及一个RNA测序表达数据集（GSE62944包括所有三种癌症类型）。使用R语言中的LIMMA统计软件包在每种单独的癌症类型中鉴定差异表达基因（DEG），然后对所得基因列表进行比较以鉴定不同癌症类型中的共同DEG。分别对微阵列和RNA测序数据集进行此分析，揭示了分别与这三种癌症相关的一组62个和1290个差异表达基因。在这些基因中，有44个在两种分析中是共同的，因此被称为关键基因。使用基因本体功能注释、京都基因与基因组百科全书通路映射和文献引用确认关键基因在癌症中的作用。最后，使用R语言中的meta软件包中的统计量探索关键基因表达的异质性。结果表明，44个关键基因中有6个表达无差异，而其余基因在微阵列样本中的表达表现出显著的异质性。总之，鉴定出的DEG可能在乳腺癌、前列腺癌和肺癌的发病机制中起重要作用，并可作为开发新型诊断和治疗策略的生物标志物。
