10.3389/fgene.2018.00422.s006
Guojun Liu
Guojun
Liu
Zihao Chen
Zihao
Chen
Irina G. Danilova
Irina G.
Danilova
Mikhail A. Bolkov
Mikhail A.
Bolkov
Irina A. Tuzankina
Irina A.
Tuzankina
Guoqing Liu
Guoqing
Liu
Table_1_Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes.docx
Frontiers
2018
muscle-invasive bladder cancer
subtypes
miR200c
miR-141
random forest
XGBoost
2018-09-28 06:38:32
Dataset
https://frontiersin.figshare.com/articles/dataset/Table_1_Identification_of_miR-200c_and_miR141-Mediated_lncRNA-mRNA_Crosstalks_in_Muscle-Invasive_Bladder_Cancer_Subtypes_docx/7145708
<p>Basal and luminal subtypes of muscle-invasive bladder cancer (MIBC) have distinct molecular profiles and heterogeneous clinical behaviors. The interactions between mRNAs and lncRNAs, which might be regulated by miRNAs, have crucial roles in many cancers. However, the miRNA-dependent crosstalk between lncRNA and mRNA in specific MIBC subtypes still remains unclear. In this study, we first classified MIBC into two conservative subtypes using miRNA, mRNA and lncRNA expression data derived from The Cancer Genome Atlas. Then we investigated subtype-related biological pathways and evaluated the subtype classification performance using Decision Trees, Random Forest and eXtreme Gradient Boosting (XGBoost). At last, we explored potential miRNA-mediated lncRNA-mRNA crosstalks based on co-expression analysis. Our results show that: (1) the luminal subtype is primarily characterized by upregulation of metabolism-related pathways while the basal subtype is predominantly characterized by upregulation of epithelial-mesenchymal transition, metastasis, and immune system process-related pathways; (2) the XGBoost prediction model is consistently robust for classification of the molecular subtypes of MIBC across four datasets (The area under the ROC curve > 0.9); (3) the expression levels of the molecules in the miR-200c and miR141-mediated lncRNA-mRNA crosstalks differ considerably between the two subtypes and have close relationships with the prognosis of MIBC. The miR-200c and miR-141-dependent mRNA-lncRNA crosstalks might be of great significance in tumorigenesis and tumor progression and may serve as the novel prognostic predictors and classification markers of MIBC subtypes.</p>