Nc2Eye: A Curated ncRNAomics Knowledgebase for Bridging Basic and Clinical Research in Eye Diseases

Abstract

Eye diseases (EDs) represent a group of disorders affecting the visual system, most of which can lead to visual impairment and blindness. Accumulating evidence reveals that non-coding RNAs (ncRNAs) are closely associated with a wide variety of EDs. However, abundant associations between ncRNAs and EDs are scattered across the published literature, obstructing a global view of ncRNA-ED associations. A public resource of high-quality manually curated ncRNAomics knowledge associated with EDs remains unavailable. To address this gap, we thus developed Nc2Eye (http://nc2eye. bio-data.cn/), which is the first knowledgebase dedicated to providing a comprehensive ncRNAomics resource for bridging basic and clinical research in EDs. Through a comprehensive review of more than 2400 published papers, Nc2Eye catalogs 7088 manually curated ncRNA-ED associations involving 4363 ncRNAs across eight species. We also provide detailed descriptions and annotation information for each ncRNAdisease association such as ncRNA categories, experimental methods, expression pattern and related clinical drugs. To further expand the pathogenic ncRNAs, we also collected more than 90 high-throughput EDs-related transcriptome datasets. Furthermore, a user-friendly interface was constructed for convenient and flexible data browsing, querying, and retrieving. We believe that Nc2Eye is a timely and valuable knowledgebase for significantly improving and useful for discovery of new diagnostic and therapeutic biomarkers.

Human microRNA similarity in breast cancer

“…Although eye disease was found in class II, similarity between breast cancer and eye disease had been not definitely demonstrated. Twenty-eight breast cancer-associated miRNAs in class II contributed to eye disease enrichment and were also found in ncRNAomics-eye disease database Nc2Eye [ 61 ]. Most miRNAs in class II have a role in age-related macular degeneration.…”

iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma

“…59 experimentally supported UM-related SGs, including mRNAs, miRNAs and lncRNAs, were retrieved from the Comparative Toxicogenomics Database 35 , the Human microRNA Disease Database 36 , miRCancer 37 , lnc2Cancer 38 , LncRNADisease 39 , and Nc2Eye 40 .…”

Computational Methods and Applications for Identifying Disease-Associated lncRNAs as Potential Biomarkers and Therapeutic Targets

“…31,32 The other two methods, TPGLDA and ncPred, allocated resources from the disease to lncRNAs and other nodes, respectively, but the difference is that the resources were returned to the initial nodes. 33,34 Recommendation Algorithm-Based Methods…”

“…Nc2Eye (http://nc2eye.bio-data.cn/) is the first high-quality manually curated ncRNAomics knowledge base associated with eye disease and includes 1,147 lncRNA-associated entries. 33 Computational Methods for Acquiring lncRNA-lncRNA Associations Most of the computational methods for inferring lncRNA-disease association are based on lncRNA-lncRNA association data. Therefore, acquiring a high-quality lncRNA-lncRNA association is critical for improving performance in predicting the lncRNA-disease association.…”