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Database for exploration of functional context of genes implicated in ovarian cancer

M. Kaur, A. Radovanovic, M. Essack, U. Schaefer, M. Maqungo, T. Kibler, S. Schmeier, A. Christoffels, K. Narasimhan, M. Choolani, V. B. Bajic
2009 Nucleic Acids Research  
Ovarian cancer (OC) is becoming the most common gynecological cancer in developed countries and the most lethal gynecological malignancy.  ...  To reduce this problem, we have developed a database dedicated to OC genes to support exploration of functional characterization and analysis of biological processes related to OC.  ...  Most of the genes implicated in OC (OC genes) have not been thoroughly investigated in the context of OC, especially at the gene regulation level.  ... 
doi:10.1093/nar/gkn593 pmid:18790805 pmcid:PMC2686485 fatcat:npialxgkwfh3vkuo6g4ogrwy34

Integrative analysis of common genes and driver mutations implicated in hormone stimulation for four cancers in women

Salma Begum Bhyan, YongKiat Wee, Yining Liu, Scott Cummins, Min Zhao
2019 PeerJ  
Using a total of 460 endometrial, 2,068 ovarian, 2,308 breast and 537 cervical cancer-implicated genes, we identified 52 genes which are common in all four types of cancers in women.  ...  Furthermore, we defined their potential functional role in endogenous hormonal regulation pathways within the context of four cancers in women.  ...  (ii) OCGene : an online database for in-depth analysis of ovarian cancer genes.  ... 
doi:10.7717/peerj.6872 pmid:31205821 pmcid:PMC6556371 fatcat:tnjetiextrcl3lsyhsqmhymbqq

Integrative analysis to identify oncogenic gene expression changes associated with copy number variations of enhancer in ovarian cancer

Xiaoyan Li, Yining Liu, Jiachun Lu, Min Zhao
2017 OncoTarget  
To learn more about the relationship between enhancers and cancer, we integrated the CNVs data on enhancers and explored their targeting gene expression pattern in high-grade ovarian cancer.  ...  We also identified 18 targeting genes by super-enhancers with prognostic significance for ovarian cancer, such as the tumour suppressor CDKN1B.  ...  The enhancer-related regulatory network construction and visualization To explore the regulatory genes of super-enhancers in a pathway context, we extracted protein-protein interaction data for the 210  ... 
doi:10.18632/oncotarget.21227 pmid:29207666 pmcid:PMC5710946 fatcat:ajg2ozaprvd6pfs3jwtqryz5kq

The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

Naiade Calanca, Cecilie Abildgaard, Cláudia Aparecida Rainho, Silvia Regina Rogatto
2020 Cancers  
In this review, we described the potential of lncRNAs for clinical applications in ovarian cancer (OC).  ...  We manually curated databases and used bioinformatics tools to identify lncRNAs implicated in the epigenetic regulation, along with examples of direct interactions between the lncRNAs and proteins of the  ...  Thus, FAL1 has an oncogenic function in OC partly exerted by the epigenetic regulation of p21 expression levels, hinting at potential implications for cancer therapy [84] .  ... 
doi:10.3390/cancers12092701 pmid:32967233 pmcid:PMC7563210 fatcat:so7rj7275vb6fnlihwiejog6qq

Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis

Ke Zhang, Xiangjun Kong, Guangde Feng, Wei Xiang, Long Chen, Fang Yang, Chunyu Cao, Yifei Ding, Hang Chen, Mingxing Chu, Pingqing Wang, Baoyun Zhang
2018 Journal of Ovarian Research  
In addition, gene ontology (GO) functional and pathway enrichment analyses of the DEGs in the most remarkable module were performed using Database for Annotation, Visualization and Integrated Discovery  ...  Furthermore, functional enrichment analysis revealed that these genes were mainly involved in the proliferation of ovarian cancer cells, such as regulation of cell proliferation, cell adhesion, positive  ...  Therefore, exploring the effect of hypoxia on ovarian cancer cells will likely have important implications and offer opportunities to solve this problem for potential therapeutic purposes.  ... 
doi:10.1186/s13048-018-0388-x pmid:29482638 pmcid:PMC5828062 fatcat:4zxrylok5ndibdjjfqdwh72iom

Mutational analysis of Polycomb genes in solid tumours identifies PHC3 amplification as a possible cancer-driving genetic alteration

F Crea, L Sun, L Pikor, P Frumento, W L Lam, C D Helgason
2013 British Journal of Cancer  
Polycomb group genes (PcGs) are epigenetic effectors implicated in most cancer hallmarks. The mutational status of all PcGs has never been systematically assessed in solid tumours.  ...  This aberration predicts poorer prognosis in lung and uterine carcinomas (Po0.01). Gene amplification correlates with mRNA overexpression (Po0.01), suggesting a functional role of this aberration.  ...  ACKNOWLEDGEMENTS We thank Kelsie L Thu for helping with data analyses and for insightful discussions.  ... 
doi:10.1038/bjc.2013.454 pmid:23942079 pmcid:PMC3776977 fatcat:hamrk5f5kjbzndbgs23hhfskky

Troponin through the looking-glass: emerging roles beyond regulation of striated muscle contraction

Jamie R. Johnston, P. Bryant Chase, Jose Renato Pinto
2017 OncoTarget  
However, mounting evidence points to novel cellular functions of troponin, with profound implications in cancer, cardiomyopathy pathogenesis and skeletal muscle aging.  ...  , particularly in the context of human disease and aging.  ...  We would like to acknowledge Jodi Slade (Slade Illustration) for the illustration in Figure 4 and the Human Protein Atlas (www.proteinatlas.org) for providing an open access database for use in publication  ... 
doi:10.18632/oncotarget.22879 pmid:29416706 pmcid:PMC5787451 fatcat:ttvconp6lbazzn6e3xnzwqkqqa

Exploration of the Role of m6 A RNA Methylation Regulators in Malignant Progression and Clinical Prognosis of Ovarian Cancer

Qinglv Wei, Dan Yang, Xiaoyi Liu, Hongyan Zhao, Yu Yang, Jing Xu, Tao Liu, Ping Yi
2021 Frontiers in Genetics  
In conclusion, m6A RNA methylation regulators are associated with the malignant progression of ovarian cancer and could be a potential in prognostic prediction for ovarian cancer.  ...  Ovarian cancer is the most deadly gynecologic malignancy worldwide and it is warranted to dissect the critical gene regulatory network in ovarian cancer.  ...  demonstrated that m 6 A modification is implicated in ovarian cancer TME.  ... 
doi:10.3389/fgene.2021.650554 pmid:34149801 pmcid:PMC8209520 fatcat:32gydqnvvfe3xdgz4f7ftlok5m

Upregulation of NEK2 is associated with drug resistance in ovarian cancer

XIA LIU, YUTAO GAO, YI LU, JIAN ZHANG, LI LI, FUQIANG YIN
2013 Oncology Reports  
In the present study, on the basis of microarray results from Oncomine and the GEO Profiles online database, we revealed that NEK2 mRNA expression in ovarian cancer tissues is upregulated.  ...  The association of NEK2 with drug resistance in ovarian cancer has not yet been reported.  ...  Acknowledgements The present study was supported by the National Natural Science Foundation of China (grant no. 81302283) and the Youth Science Foundation of Guangxi Medical University (no.  ... 
doi:10.3892/or.2013.2910 pmid:24337664 fatcat:fn4hhkbuungt7igyuaw5nf2i5y

Increased expression of TET3 predicts unfavorable prognosis in patients with ovarian cancer-a bioinformatics integrative analysis

Tiefeng Cao, Wenwei Pan, Xiaoli Sun, Huimin Shen
2019 Journal of Ovarian Research  
The TET3 expression in ovarian cancer was assessed with Oncomine database, and validated with TCGA and GTEx database.  ...  Previous studies indicated that TET3 is overexpressed in ovarian cancer tissues. However, the clinic-pathological functions and prognostic values of TET3 remain unclear.  ...  Acknowledgments We are grateful for the contribution of all databases including TCGA, GTEx, GEO, Oncomine, Kaplan-Meier plotter, PrognoScan, cBioPortal data, STRING analysis and ICGC that provide free  ... 
doi:10.1186/s13048-019-0575-4 pmid:31656201 pmcid:PMC6816171 fatcat:j4jgymxc25emnle6u2gwnsnjqa

Downregulation of NEK11 is associated with drug resistance in ovarian cancer

XIA LIU, YUTAO GAO, YI LU, JIAN ZHANG, LI LI, FUQIANG YIN
2014 International Journal of Oncology  
To our knowledge, this is the first report of the association of NEK11 with drug resistance in cancer, and it would pave the way for further investigation of the drug resistance-related functions of this  ...  NEKs [NIMA (never in mitosis gene A)-related expressed kinase] are involved in ovarian cancer development and progression, while their association with drug resistance is limited, especially NEK11, and  ...  Thus, mining and exploring of potentially drug resistance-related genes would be a feasible and reasonable way to meet the challenge of the drug resistance in ovarian cancer (9) .  ... 
doi:10.3892/ijo.2014.2503 pmid:24969318 fatcat:3pbultjysvg35b2mwl5sk6rokq

An overview of long non-coding RNAs in ovarian cancers

Matthieu Meryet-Figuière, Bernard Lambert, Pascal Gauduchon, Nicolas Vigneron, Emilie Brotin, Laurent Poulain, Christophe Denoyelle
2016 OncoTarget  
Together, the available information suggests that the emerging field of lncRNAs will pave the way for a better understanding of ovarian cancer biology and might lead to the development of innovative therapeutic  ...  As with miRNAs a decade ago, the scientific community recently understood that lncRNAs represent a new layer of complexity in the regulation of gene expression.  ...  Research), the University of Caen Normandy and the Comprehensive Cancer Center F.  ... 
doi:10.18632/oncotarget.8089 pmid:26992233 pmcid:PMC5190131 fatcat:kxmbh2h6qzd5hpyxkjkmjfvc5a

Bioinformatics analysis of dysregulated microRNAs in the nipple discharge of patients with breast cancer

Kai Zhang, Ya-Wen Wang, Rong Ma
2017 Oncology Letters  
The aim of the present study was to explore the potential functions of miRNAs in the development of breast cancer using bioinformatics analysis, based on the miRNA expression profile in nipple discharge  ...  In the present study, the target genes of miR-3646, -4484 and -4732-5p were predicted using TargetScan and the MicroRNA Target Prediction and Functional Study Database.  ...  The authors thank Cloud-Seq Company (Shanghai, China) for the technical assistance in bioinformatic analysis.  ... 
doi:10.3892/ol.2017.5801 pmid:28521415 pmcid:PMC5431374 fatcat:a3k4fzboane55j6mo57ephaazu

BaySyn: Bayesian Evidence Synthesis for Multi-system Multiomic Integration [article]

Rupam Bhattacharyya, Nicholas Henderson, Veerabhadran Baladandayuthapani
2022 medRxiv   pre-print
Our mechanistic models implicate several relevant functional genes across cancers such as PTPN6 and ERBB2 in the KEGG adherens junction gene set.  ...  of known lineage-specific biomarker associations such as BCL11A in breast and FGFRL1 in ovarian cancers.  ...  Different upstream mechanisms of the ERBB2 gene have been implicated in different gynecological cancers, such as copy number changes in ovarian tumors 38 and somatic mutations in breast cancer. 39 he  ... 
doi:10.1101/2022.08.16.22278812 fatcat:gyakrsuabzdozactyipyzgsx3y

Association between the expression of secreted phosphoprotein - related genes and prognosis of human cancer

Yaqin Tu, Cai Chen, Guorun Fan
2019 BMC Cancer  
The STRING database was used to generate a Protein - Protein Interaction (PPI) network for SPP genes.  ...  While many studies have assessed the predictive value of secreted phosphoprotein (SPP) genes in cancer, the findings have been inconsistent.  ...  Acknowledgements The authors would like to thank all publicly available data used in the present study.  ... 
doi:10.1186/s12885-019-6441-3 pmid:31849319 pmcid:PMC6918603 fatcat:m4f25ef5ubg6vbvos2hzkogxiu
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