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NSDNA overview
• NSDNA is a comprehensive database linking ncRNAs and NSDs. NSDNA provides experimentally supported ncRNA-NSD associations. The current version of NSDNA documents 26128 (21384 miRNA-, 4608 lncRNA-, 13 siRNA-, 16 snoRNA- and 107 piRNA-associated entries) associations between 8736 ncRNAs and 144 NSDs in 11 species (Figure 1), following manual curation of 1410 articles.
• NSDNA offers 1)
Browse and 2)
Search pages as well as downloadable lists of ncRNA-NSD associations. 3) The
Links page provides some useful ncRNA and NSD-related links for users. 4) The
Download page allows users to download the ncRNA-NSD association data. 5) The
Submit page provides a submission function for researchers to submit novel ncRNA-NSD associations that are not documented in NSDNA. NSDNA will check submissions as soon as possible. 6)
Prioritize ncRNA in the certain tissue and disease.
• Please select
Help for more details on
NSDNA.
Browse help
The Browse page allows users to browse the NSDNA database. The "file tree" contains 8 branches on the left panel: miRNAs, lncRNAs, siRNAs, snoRNAs, piRNAs, diseases, species and tissues. By clicking on a particular tree node, a corresponding dataset will be displayed on the right panel. Clicking on "click here to download" allows the user to download the browsing results (Figure 2).
Search help
• The Search page allows users to input keywords for different purposes. Users can input a miRNA/lncRNA/siRNA/snoRNA/piRNA/disease/tissue name to query related associations in NSDNA (Figure 3-[1]). Users can select all species or particular species from the species pull-down menu (Figure 3-[2]). NSDNA allows users to choose high throughput or low throughput experimental data or both (Figure 3-[3]). NSDNA supports “fuzzy” keyword searching capabilities that allows for easy searching by returning the closest possible matching records.
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NSDNA data table When users input keywords in the query textbox and press the "search" button, corresponding results are displayed. NSDNA results are organized in a data table, with a single association record on each line that contains the following information: ncRNA name, disease name, expression pattern, species, tissue and PubMed ID. Users can then click on the "Details" button to view more detailed information of a particular association. Users can click on "click here to download" to download the data table (Figure 4).
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NSDNA details Users can obtain detailed NSDNA information by clicking on the “Details” button of the data table. The Details page contains more comprehensive information for a given record, including disease name, ncRNA name, expression pattern, species, detection methods, ncRNA targets, tissue or cell lines for detection, treatment-influenced ncRNA expression, PubMed ID, publication year and detailed description in the reference (Figure 5).
Download help
• The Download page allows users to download experimentally supported ncRNA-NSD association data. Users can download all miRNA-NSD, lncRNA-NSD, siRNA-NSD, snoRNA-NSD and piRNA-NSD association data in text or excel formats. NSDNA also provides different types of downloadable files. Users can download circulating miRNA, treatment-associated miRNA and miRNA-target association data from NSDNA. NSDNA also allows users to download ncRNA-NSD association data from diverse species such as Homo sapiens, Mus musculus and Rattus norvegicus.
• The database is regularly updated; to download the latest dataset, please send a request to wanglh211@163.com.
Submission help
In the Submit page, NSDNA invites users to submit novel ncRNA-NSD association data. Users need to provide certain information that describes the potential associations. Users are required to fill the textboxes containing a "*". Once approved by the submission review committee, the submitted record will be included in the database and made available to the public in the following release (Figure 6).
Prioritization help
• NSDNA provides users a prioritization page that enables researchers to prioritize ncRNAs in a specific tissue and disease. For miRNAs, we used low-throughput experiments confirmed miRNA as the gold standard and prioritize the set of miRNAs supported by high-throughput experiments based on semantic similarities of functional genomic data as previously described (1). In brief, this prioritized method ranked candidate miRNAs according to their semantic similarity and distance proximity to the gold standard. For lncRNAs, we used low-throughput experiments confirmed lnRNA as the gold standard and prioritize the set of lncRNAs supported by high-throughput experiments based on functional similarity as previously described (2). Finally, we integrated the tool and the prioritized results into the NSDNA database.
• Users can select a particular disease, ncRNA category and tissue from the pull-down menu. By pressing the "prioritize" button, corresponding scores of ncRNA in specific tissues and diseases are displayed. The higher scores of a certain ncRNA indicate increased value in the specific tissue and disease. For example, by prioritizing the miRNAs in the brain of Alzheimer disease, NSDNA shows the scores of miRNAs. The top 5 miRNAs are hsa-miR-633, hsa-miR-181d, hsa-miR-485-5p, hsa-miR-146b-3p, and hsa-miR-208b, and hsa-miR-633 had the highest score of 5.414 (Figure 7). We hope that this prioritization tool will improve the performance of NSDNA, making it increasingly useful for biologists to perform future studies.
• References
1. Wang, P., Ning, S., Wang, Q., Li, R., Ye, J., Zhao, Z., Li, Y., Huang, T. and Li, X. (2013) mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PLoS One, 8, e53685.
2. Wang, P., Ning, S., Zhang, Y., Li, R., Ye, J., Zhao, Z., Zhi, H., Wang, T., Guo, Z. and Li, X. (2015) Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res, 43, 3478-3489.
Frequently Asked Questions
1. How often will the database be updated?
• We attempt to update the database as frequently as possible. Currently, NSDNA is updated quarterly with data from PubMed publications.
2. Do you plan to offer more services?
• We will do our best to provide users with more quality services. In the future, we plan to provide additional tools, such as sequence analysis tool and ncRNA-NSD association prediction tool.
• For services you hope to see in NSDNA, please kindly e-mail us to provide suggestions.
3. Why are some published ncRNA-NSD associations not found in NSDNA?
• The data in NSDNA has been curated from published articles up to Jun 15, 2016. Any ncRNA-NSD association found after Jun 15 has not yet been documented.
• The data in NSDNA is manually curated, and omissions cannot be avoided.
• Please submit undocumented ncRNA-NSD associations via the “submit” page.
4. How this database is comprehensive than other similar databases?
• Currently, several ncRNAs (mainly miRNAs and lncRNAs) associated databases were established, such as miR2Disease, HMDD and LncRNADisease. These databases are crucial for studying ncRNA functions in human diseases.
• However, to the best of our knowledge, none of these resources were developed to specifically collect experimentally supported NSD-ncRNA association data. For example, miR2Disease only documents 450 NSD-related entries of associations between 179 miRNAs and 26 NSDs, while LncRNADisease only includes 196 NSD-related entries of associations between 74 lncRNAs and 37 NSDs, and only human data are available in these databases. NSDNA contains general NSDs, nearly 6 and 4 times the number of NSDs than the miR2Disease and LncRNADisease databases, respectively. Compared with miR2Disease, NSDNA also includes data regarding mutations in ncRNA and their association with NSDs. Moreover, miR2Disease has not been updated since 2009.
• NSDNA has several advantages compared to previous studies. First, NSDNA includes many ncRNAs categories (miRNAs, lncRNAs, siRNAs, snoRNAs and piRNAs), while the above-mentioned databases only include one ncRNA category. Second, NSDNA includes data for many species, and users can retrieve and download all species or particular species data. Third, data on NSD-associated circulating miRNA, treatment-associated miRNA and miRNA target were also added to the NSDNA.
• The detail statistics are listed in the following table.
