Wnt pathway gene expression and association with clinicopathologic characteristics in endometrial cancer – An analysis of The Cancer Genome Atlas (TCGA)

2013 ◽  
Vol 130 (1) ◽  
pp. e89 ◽  
Author(s):  
T. Dellinger ◽  
C. Warden ◽  
E. Han ◽  
M. Wakabayashi
Keyword(s):  
Gene Expression ◽  
Endometrial Cancer ◽  
Wnt Pathway ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Clinicopathologic Characteristics ◽  
Pathway Gene ◽  
Cancer Genome Atlas ◽  
Genome Atlas

scholarly journals Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas

2018 ◽  
Author(s):  
SR Rosario ◽  
MD Long ◽  
HC Affronti ◽  
AM Rowsam ◽  
KH Eng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Flux ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Targeted Therapeutics ◽  
Bioinformatics Pipeline ◽  
Metabolic Dysregulation ◽  
Pathway Gene ◽  
Cancer Genome Atlas ◽  
Genome Atlas

AbstractUnderstanding the levels of metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Using transcriptomic data from 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we developed a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. This pathway dysregulation was confirmed in separate patient populations, further demonstrating the robustness of this approach. A bootstrapping simulation was then applied to assess whether these alterations were biologically meaningful, rather than expected by chance. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest in both common and rare disease sites. Utilizing a pathway mapping approach to understand patterns of metabolic flux, differential drug sensitivity, can accurately be predicted. Further, the identification of Master Metabolic Transcriptional Regulators, whose expression was highly correlated with pathway gene expression, explains why metabolic differences exist in different disease sites. We demonstrate these also have the ability to segregate patient populations and predict responders to different metabolism-targeted therapeutics.

scholarly journals Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas

Oncotarget ◽  
2018 ◽  
Vol 9 (24) ◽  
pp. 17093-17103 ◽  
Author(s):  
David S. Guttery ◽  
Kevin Blighe ◽  
Konstantinos Polymeros ◽  
R. Paul Symonds ◽  
Salvador Macip ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Racial Differences ◽  
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.

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