INTRODUCTION:

What is ncEP?

ncEP is a database for ncRNA-encoded proteins or peptides which were validated by low-throughput experiments from published papers. ncEP database contains features for the peptides or proteins encoded by ncRNAs on their names, sequences, experimental species, genomic locations, experimental tissues or cell lines, data source and other detailed information.

Why to create ncEP database?

NcRNAs could take part in amounts of biological processes such as cell growth, development, metabolism, death and so on. Initially, these ncRNAs were merely regarded as “untranslated” RNAs. Recently, it was demonstrated that ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and primary miRNAs (pri-miRNAs), could also be translated into proteins or peptides, which usually contain less than 100 amino acids. From then on, several approaches have been proposed to high-throughput predict proteins or peptides encoded by ncRNAs. However, it lacks a gold standard set of ncRNA-encoded proteins or peptides, because the low-throughput experimentally validated peptides scattered in a large amount of publications without systematic records. We hope that this elaborate database, specially designed for ncRNA-encoded proteins or peptides, could enrich knowledge of the ncRNA translation.

What does ncEP database contain?

ncEP database contains low-throughput experimentally validated proteins or peptides encoded by ncRNAs, from published articles. Each entry includes the detailed information about protein or peptide name, experimental species, chromosome location, protein or peptide sequence, protein or peptide length, ncRNA type, ncRNA name, experimental techniques, experimental samples (cell line and/or tissue), subcellular location, protein or peptide function, reference information (PubMed ID, year of publication, title of paper) and so on. Collectively, ncEP include 80 entries that include proteins or peptides encoded by 22 lncRNAs, 9 circRNAs, 9 pri-miRNAs and 37 other non-coding RNAs across 18 species from more than 50 papers. In addition, ncEP provides an online genome browser to show the genome locations of ncRNAs and proteins or peptides as well as their species conservations.

SEARCH:

1. Search by protein or peptide name.

If you want to query a protein or peptide by name, e.g. Mtln, you can select "Mtln" from the dropdown list of protein or peptide name and press "Search" button (Fig 1). The results list all potential entries related to your inputted "Mtln". The basic information about the proteins or peptides and ncRNAs is returned (Fig 2).Then click "more", you can get the detailed information.

Fig 1. Search by protein or peptide name.

Fig 2. The search result of "Mtln".

2. Search by ncRNA name.

Example: If you want to query a ncRNA, which can encode a protein or peptide, e.g. LINC00948, you should select the ncRNA name "LINC00948" from the ncRNA name pull-down menu (Fig 3). The results list all potential entries related to your inputted "LINC00948". The basic information about the proteins or peptides and ncRNAs are returned (Fig 4). Then click "more", you can get the detailed information.

Fig 3. Search by ncRNA name.

Fig 4. The search result of "LINC00948".

3. Search by genome location.

You can query the protein or peptide by genome location. Firstly, you can select species from the species dropdown list, such as "Homo sapiens (human)". Then, select chromosome number from the chromosome dropdown list, such as "4". Next, you should input genome start site such as "152321585" and end site such as "164899063" in the query textbox and press "Search" button (Fig 5). The results list all potential entries related to your inputted "Homo sapiens (human)", "4", "152321585" and "164899063". The basic information about the proteins or peptides and ncRNAs is returned (Fig 6). Furthermore, click "more", you can get the detailed information.

Fig 5. Search by genome location.

Fig 6. The search result of "Homo sapiens (human)", "4", "152321585" and "164899063".

BROWSE：

ncEP includes 18 species such as "Homo sapiens (human)", "Mus musculus", "Danio rerio (zebrafish)" and so on (Fig 7). You can browse any species, which you are interested in, e.g. Homo sapiens (human). Then, click on the species picture and all entries related to your choose "Homo sapiens (human)" are returned (Fig 8). Next, click "more", you can get the detailed information.

Fig 7. Browse all species in ncEP.

Fig 8. The browse result of "Homo sapiens (human)".

Genome browser:

ncEP has also integrated an online genome browser for visualization of the genome locations of the proteins or peptides, ncRNAs and species conservation information in the track. Firstly, you can select species e.g. Homo sapiens (human) from the species dropdown list. Then, select proteins or peptide name e.g. CASIMO1, from the protein or peptide name dropdown list (Fig 9). Next, you can click "Submit" to get genome locations of ncRNA, protein or peptide and species conservation information (Fig 10). ncRNAs, peptides and species conservation information are shown as three independent tracks in genome browser. If you do not know the name of protein or peptide or ncRNA, you can also search in ncEP based on its genome location in genome browser.

Fig 9. Select species "Homo sapiens (human)" and protein or peptide name "CASIMO1".

Fig 10. The result of "Homo sapiens (human)" and "CASIMO1".

Download and Submit:

ncEP has provided "DOWNLOAD" and "SUBMIT" interfaces for users download all data about ncRNA-encoded proteins or peptides in formation in a tab-separated file and submit new ncRNA-encoded proteins or peptides in formation (Fig 11and 12).

Fig 11. "DOWNLOAD" interface for "file with ncRNA-encoded proteins or peptides information".

Fig 12. "SUBMIT" interface for new ncRNA-encoded proteins or peptides information.