CDRC DB

About CDRCdb

CDRCdb is a multi-omics database for companion animals and humans. It provides researchers with a foundation for integrated multi-omics analysis on companion animals. It offers preprocessed data from WGS, RNA-seq, ChIP-seq, ATAC-seq, MBD-seq along with their phenotypes. Besides supplying the data, CDRCdb also provides a visual representation of the overall projects and individual researcher’s project statuses that are utilizing the database, and aids in conducting more efficient analyses at a group level. Such a database is ideally suited for research in comparative medicine and will also assist in conducting other studies related to companion animals.

About CDRC
CDRC stands for Comparative Medicine Disease Research Center, which conducts studies comparing and researching naturally occurring animal disease models with human diseases to understand the etiology of the human body. Furthermore, it develops core technologies to better understand disease mechanisms through comparative genetic and non-epigenetic approaches to diseases in dogs and humans and proposes solutions for these diseases.
ACHIEVEMENTS
Multi-targeted therapy resistance via drug-induced secretome fucosylation
Multi-targeted therapy resistance via drug-induced secretome fucosylation

Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post- translational cancer hallmark and the consequences thereof remain elusive. Here we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In cancer cell cultures, xenograft mouse models, and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycoproteomes identified fucosylation of the antioxidant PON1 as a critical component of the therapy-induced secretome (TIS). N-glycosylation of TIS and target core fucosylation of PON1 are mediated by the fucose salvage-FUT8-SLC35C1 axis with PON3 directly modulating GDP-Fuc transfer on PON1 scaffolds. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Global and PON1-specific secretome de-N-glycosylation both limited the expansion of resistant clones in a tumor regression model. We defined the resistance-associated transcription factors (TFs) and genes modulated by the N-glycosylated TIS via a focused and transcriptome-wide analyses. These genes characterize the oxidative stress, inflammatory niche, and unfolded protein response as important factors for this modulation. Our findings demonstrate...

2023.03.31 | 논문
Elife | 2023 | 12 | 1
Rex: R-linked EXcel add-in for statistical analysis of medical and bioinformatics data
Rex: R-linked EXcel add-in for statistical analysis of medical and bioinformatics data

Background Microsoft Excel has substantial functionalities for data management and analyses, and has been the most popular software in this field. However, in spite of Excel’s user-friendly interface and functionality for data management, it provides very few functions for in-depth statistical analyses, which has limited its wider application for this purpose. Objective Here, we introduce Rex, an Excel add-in software implementing the powerful analytical and graphical functions of R within Excel. Methods Rex was implemented using three types of programming software: R, JavaScript, and Microsoft VB.Net. Results Rex provides a graphical user interface (GUI) through Excel, and statistical analysis can be conducted by pointing and clicking the menu without programming R. Rex covers a wide range of analyses from basic statistics to advanced analysis, including structural equation modeling, complex sampling design, and machine learning models, making it possible for researchers not skilled in using a command-line interface to conduct in-depth statistical analyses. Most Rex modules are available in a free version for non-commercial use, and it can be used for educational and public purposes. Conclusion In this article, we introduce the framework and features of Rex with illustrative examples of its implementation.

2023.03.31 | 논문
Genes & Genomics | 2023 | 45 | 1
DB status