scholarly journals Identification of prognostic miRNA biomarkers for esophageal cancer based on The Cancer Genome Atlas and Gene Expression Omnibus

Medicine ◽  
2021 ◽  
Vol 100 (7) ◽  
pp. e24832
Author(s):  
Jinru Xue ◽  
Erna Jia ◽  
Na Ren ◽  
Hua Xin
Keyword(s):  
Gene Expression ◽  
Esophageal Cancer ◽  
Gene Expression Omnibus ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals The role of miR-92b in cholangiocarcinoma patients

2018 ◽  
Vol 33 (3) ◽  
pp. 293-300 ◽  
Author(s):  
Min-hang Zhou ◽  
Hong-wei Zhou ◽  
Mo Liu ◽  
Jun-zhong Sun
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Gene Expression Omnibus ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Positive Regulation ◽  
Cancer Genome Atlas ◽  
High Level ◽  
Genome Atlas

Purpose: The role of microRNA (miRNA) in cholangiocarcinoma was not clear. The aim of this study was to find the potential diagnostic and prognostic miRNA in cholangiocarcinoma patients. Methods: The miRNA expression profiles in cholangiocarcinoma patients from The Cancer Genome Atlas and Gene Expression Omnibus (GSE53870) were analyzed. The comparison of overall survival was performed using the Kaplan–Meier method. The targeted genes of prognostic miRNA were identified in miRanda, PicTar, or TargetScan, and their cell signaling pathways were analyzed by the Database for Annotation, Visualization and Integrated Discovery. Results: In The Cancer Genome Atlas and the Gene Expression Omnibus miRNA dataset, miR-92b and miR-99a were found with concordant directionality, up-regulated and down-regulated, respectively. In The Cancer Genome Atlas survival data, patients with the high level of miR-99b had obviously shorter overall survival time ( P=0.038). However, the level of miR-99a was not found to be significant. The 17 shared target genes of miR-92b were identified, such as DAB21IP, BCL21L11, SPHK2, PER2, and TSC1. The related pathways included positive regulation of transcription, positive regulation of cellular biosynthetic process, regulation of programmed cell death, etc. Conclusion: miR-92b was up-regulated in cholangiocarcinoma compared with normal controls. The high level of miR-92b was associated with adverse outcomes in cholangiocarcinoma patients, which might be partly explained by the targeted genes of miR-92b and their signaling pathways.

Using machine learning method to identify MYLK as a novel marker to predict biochemical recurrence in prostate cancer

2021 ◽  
Vol 15 (1) ◽  
pp. 29-41
Author(s):  
Peng Qiao ◽  
Di Zhang ◽  
Song Zeng ◽  
Yicun Wang ◽  
Biao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Biochemical Recurrence ◽  
Surgical Margin ◽  
Gene Expression Omnibus ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Support Vector ◽  
Cancer Genome Atlas ◽  
Genome Atlas

Aim: This study aims to identify novel marker to predict biochemical recurrence (BCR) in prostate cancer patients after radical prostatectomy with negative surgical margin. Materials & methods: The Cancer Genome Atlas database, Gene Expression Omnibus database and Cancer Cell Line Encyclopedia database were employed. The ensemble support vector machine-recursive feature elimination method was performed to select crucial gene for BCR. Results: We identified MYLK as a novel and independent biomarker for BCR in The Cancer Genome Atlas training cohort and confirmed in four independent Gene Expression Omnibus validation cohorts. Multi-omic analysis suggested that MYLK was a DNA methylation-driven gene. Additionally, MYLK had significant positive correlations with immune infiltrations. Conclusion: MYLK was identified and validated as a novel, robust and independent biomarker for BCR in prostate cancer.

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