Comparative analysis of oncogenes identified by microarray and RNA-sequencing as biomarkers for clinical prognosis.
OBJECTIVE
Although RNA-sequencing has been widely used to identify the differentially expressed genes (DEGs) as biomarkers to guide the therapeutic treatment, it is necessary to investigate the concordance of DEGs identified by microarray and RNA-sequencing for the clinical prognosis.


METHODS
By using The Cancer Genome Atlas data sets, we thoroughly investigated the concordance of DEGs identified from microarray and RNA-sequencing data and their molecular functions.


RESULTS
The DEGs identified by both technologies averaged ~98.6% overlap. The cancer-related gene sets were significantly enriched with the DEGs and consistent between two technologies.


CONCLUSIONS
The highly consistency of DEGs in their regulation directionality and molecular functions indicated the good reproducibility between microarray and RNA-sequencing in identifying potential oncogenes for clinical prognosis.
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Yuan
Y
Liu
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Runyu
R
Jing
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Junmei
J
Xu
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Keqin
K
Liu
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Jiwei
J
Xue
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Zhining
Z
Wen
College of Chemistry, Sichuan University, Chengdu 610064, PR China.
Menglong
M
Li
D014408:Biomarkers, Tumor / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D009857:Oncogenes / Q000235:genetics*; D011379:Prognosis; D017423:Sequence Analysis, RNA
D014408:Biomarkers, Tumor
DNA microarray; RNA-sequencing; cancer prognosis; comparative analysis; enrichment analysis; molecular function; oncogene