Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer

BMC Bioinformatics
Keqin LiuMenglong Li

Abstract

Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for the classification of histological subtypes and the prediction of clinical outcomes. However, the impact of non-significantly mutated genes (non-SMGs), which may also play important roles in the prognosis of EC patients, has not been extensively studied. Therefore, it is essential for the discovery of biomarkers in ECs to further investigate the non-SMGs that were highly associated with clinical outcomes. For the 9681 non-SMGs reported by the mutation annotation pipeline, there were 1053, 1273 and 395 non-SMGs differentially expressed between the patient groups divided by the clinical endpoints of histological grade, histological type as well as the International Federation of Gynecology and Obstetrics (FIGO) stage of ECs, respectively. In the gene set enrichment analysis, the cancer-related pathways, namely neuroactive ligand-receptor interaction signaling pathway, cAMP signaling pathway and calcium signaling pathway, were significantly enriched with the differentially expressed non-SMGs for all the three endpoints. We fu...Continue Reading

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Citations

Jun 7, 2019·Journal of Cellular Biochemistry·Dong OuyangXueqiong Zhu

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

VCPA
MATLAB
SIFT
libsvm3
PolyPhen2
Polymorphism Phenotyping ( PolyPhen2 )
Annotate Variation ( ANNOVAR )
Database for and Integrated Discovery ( DAVID )

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