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BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery

Hayley M Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Kahsay
2017 Nucleic Acids Research  
Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery.  ...  BioMuta, a database of cancer-associated single-nucleotide variations, and BioXpress, a database of cancer-associated differentially expressed genes and microRNAs, differ from other disease-associated  ...  ACKNOWLEDGEMENTS The authors would like to thank Dan Crichton for his assistance in linking to these resources from the EDRN portal,  ... 
doi:10.1093/nar/gkx907 pmid:30053270 pmcid:PMC5753215 fatcat:fb46akauljfjpfy5ibqmltirvi

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

Hayley M. Dingerdissen, Frederic Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi, Amanda Bell, Nikhita Gogate, Samir Gupta, Evan Holmes, Robel Kahsay, Jonathon Keeney, Heather Kincaid, Charles Hadley King (+3 others)
2020 JCO Clinical Cancer Informatics  
METHODS Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker  ...  Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both  ...  Data were pulled from external consortium databases for public biomarker data from EDRN, 10 cancer mutation data from BioMuta, 25,26 cancer differential expression of mRNA and miRNA from BioXpress, 26  ... 
doi:10.1200/cci.19.00117 pmid:32142370 pmcid:PMC7101249 fatcat:qijqv25waffovfheo77vm7meey

Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer

Ting-Chia Chang, Santosh Goud, John Torcivia-Rodriguez, Yu Hu, Qing Pan, Robel Kahsay, Jonas Blomberg, Raja Mazumder, Robert Belshaw
2019 PLoS ONE  
This study provides a list of mutational hotspots in HERVs, which could potentially be used as biomarkers and therapeutic targets.  ...  Human endogenous retroviruses (HERVs) have been investigated for potential links with human cancer.  ...  Acknowledgments The authors would also like to thank Hiral Desai for review and critical feedback. Author Contributions  ... 
doi:10.1371/journal.pone.0213770 pmid:30934003 pmcid:PMC6443178 fatcat:lxp4ilkbofbt5jcgy7ukycxm2a

Identification of key regulators in Prostate cancer from gene expression datasets of patients [article]

Irengbam Rocky Mangangcha, Md. Zubbair Malik, Ömer Küçük, Shakir Ali, R. K. Brojen Singh
2019 bioRxiv   pre-print
Identification of key regulators and regulatory pathways is an important step in the discovery of genes involved in cancer.  ...  Here, we propose a method to identify key regulators in prostate cancer from a network constructed from gene expression datasets of PCa patients.  ...  BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Research, gkx907. 14.  ... 
doi:10.1101/643643 fatcat:7wr4ajdnzrhbpjzbojh6eub7ka

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
2019 Frontiers in Pharmacology  
This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data.  ...  , types of in vitro, in vivo,-clinical or other data recorded and suitability for modelling, read-across, or similarity searching.  ...  Whereas, CancerResource focuses on cancer related drug-target interactions, expression, and mutation data as well as drug sensitivity data.  ... 
doi:10.3389/fphar.2019.00561 pmid:31244651 pmcid:PMC6580867 fatcat:t3junhqvxfeslcu37pihztlxiq