Q1   Get an overview of MNDR from the Home page

The homepage is displayed in the following Fig 1-1.

Fig 1-1:

1. Main functions of the database are provided in menu bar form (boxed in light green).

2. A link to our old version MNDR 1.0.

3. Other databases contributed by our group.

4. Cite information.

5. Resources integrated in MNDR.

Fig 1-1 Home page

Q2   Use the Search page to enter a keyword and filter results

The search page is displayed in Fig 2-1:

1. Carefully select a dataset: Five choices are provided.

2. Enter a keyword corresponding to selected dataset.

3. Both "Fuzzy query" and "Accurate query" are supported.

4. Four categories provided to filter results: ncRNA Category, Species, Detection Method and Score.

5. Use NCBI Gene/miRBase/Disease Ontology/MeSH to normalize your input symbol.

Fig 2-1 Search page

Q3   How to read Results

In the result page, all entries are listed with basic information including ncRNA symbols, disease name, species and score.

Fig 3-1:

1. Your current input conditions.

2. Total sum of results.

3. Click to turn the page.

4. Click to link to detail page.

5. All entries in MNDR collected from literature by our manually reading.

Fig 3-1 Result page

Q4   How to read Detail page

In the detail page, you can get information including MNDR ID, confidence score, ncRNA information, disease information, evidence support and references.

Fig 4-1:

For ncRNA-disease associations, users can choose any union of ncRNA and disease to see results.

Fig 4-1 Detail page of basic information.

Fig 4-2:

For ncRNA-disease associations, users can click miRBase Accession/EntreZ ID to see its basic description in miRBase/NCBI gene database.

Fig 4-2 Detail page of ncRNA information.

Fig 4-3:

1. Click any disease as a keyword to search in database.

2. Click Disease Ontology/MeSH ID to see its description in detail.

Fig 4-3 Detail page of disease information.

Fig 4-4:

1. Evidence Support including three parts: strong evidence, weak evidence and support database.

2. Tissue or cell line, target genes/RNAs and expression of each ncRNA.

3. Click pubmed ID to see description in detail.

Fig 4-4 Detail page of evidence support and references.

Q5   How to use Browse page in MNDR

In the browse page, you can click each node to see results.

1. 'Diseases' display all entries as long as the current selected disease is involved.

2. 'ncRNA Category' indicates all kinds of ncRNA in MNDR.

3. 'Species' display all entries as long as the organism matches the condition.

Fig 5-1 Browse page

Q6   Detailed description of the MNDR Scoring System

In MNDR v2.0, the ncRNA-disease associations are collected from different types of resources under one common framework, including experimental and prediction evidence. In principle, we assume that:

  1. Experimental evidence should contribute more important to the confidence score than prediction evidence;

   2. Strong experimental evidence should provide more reliable evidence than weak experimental evidence;

  3. ncRNA-disease associations supported by more evidence should be given significantly higher confidence scores than those supported by fewer evidence.

Similar to RAID v2.0 database, according to the evidence types and number of evidence resources, we calculate the confidence score (S) for each ncRNA-disease association as follows:

where i is the evidence type(s: strong experimental evidence, w: weak experimental evidence, p: computational prediction method), x is the number of evidence resources, we set weight factor Ws, Ww and Wp to 1, 0.65, and 0.15, respectively(if x=0, we set weight factor Wi to 0).

Q7   ncRNA and Disease Naming Conventions

Integration of source databases which use different ncRNA and disease naming conventions is challenging. To ensure maximal connectivity of data, we transform each ncRNA and disease name found in the input sources to the appropriate naming convention.

1. For miRNA, we use miRBase ID and miRBase Accession.

2. For others, we use official Gene Symbol and Entrez ID.

3. For diseases, we normalized each disease name and ID according to Disease Ontology and MeSH.

4. For species, we normalized organism names according to NCBI Taxonomy Database.

Contact wangdong@ems.hrbmu.edu.cn
© College of Bioinformatics Science and Technology, Harbin Medical University