- 1. Search Options
- 2. Component Report
- 3. My Relationship Set
- 4. Potential Biomarkers Search
- 5. An Example on How to Explore MK4MDD to Generate Hypothesis
- 6. Download & Upload
1. Search Options
There are several search options to facilitate users to access and browse the MDD data network (Figure 1):
1) Multi-level Search on the homepage: to search published reports of a component of interest in all the 7 research levels.
Multi-level Search Example
2) Advanced Search --> Genetic/Epigenetic Locus Search: to search MDD related genetic factors and epigenetic modification sites in genetic/epigenetic locus level.
Option of ‘No. of Studies’ could help user sort components with at least the specified number of studies.
For example, selecting components with at least two positive results by setting ‘Positive studies’ and inputting 2 in ‘No. of Studies’ option.
Genetic/Epigenetic Locus Search Example
3) Advanced Search --> Cross Data Search: to search relationships between different levels of components. For example, users may select the level of component A as
‘Gene’ and level of component B as ‘Brain Morphology and Function’ to study relationships between genes and brain morphology and function components.
‘Result Category’ option is also designed to help filter positive relationships.
Cross Data Search Example
2. Component Report
MK4MDD provides a detailed report for each component, which includes the following parts of information.
(a) 'Basic information'. This part includes basic information for components.
(b) 'Relationship between component and MDD'. This part presents a detailed description of the relationship between component and MDD, as well as a list of references which reported the relationship. Positive and negative relationships are presented separately.
(c) 'Relationship between component and other components at different levels'.This is to demonstrate how components are linked with each other. In this part, positive results and negative results are shown separately too.
(d) 'Data network of component'. A graphical data network, centered by the component under study and constituted of its related components which have positive results described in (b) and (c), will be generated automatically.
(e) 'Supplementary annotation'. This part of information was acquired by bioinformatic analysis, and is only available for components of SNPs, genes, proteins, and pathways.
3. My Relationship Set
To help users acquire customized data network, MK4MDD provides a unique module of ‘My Relationship Set’, which allows users to select positive relationships of interest by clicking on ‘ADD’ button from either ‘Component Report’ or search results of ‘Data Cross Search’. Both relationships of literature-origin or from supplementary annotation can be added into ‘My Relationship Set’. On ‘My Relationship Set’ page, users can do further editing on the selected relationships to generate a dynamic data network. In the graphical network, solid line represents relationship of literature-origin and dot line represents relationship from supplementary annotation.
To help users maintain their relationship set, download and upload functions were also provided. Users can store their selected relationships by using download function and upload them later for further analysis. The upload file format should be the same as the downloaded file, which is a text file containing 8 columns separated by tab. Name and description for each column is as belows:
4. Potential Biomarkers Search
To provide new clues on biomarkers, MK4MDD provides a list of potential biomarkers by analyzing the current research data. Users may search potential biomarkers by specifying the name, or defining research levels or test methods. Detailed evidence for each potential biomarker is provided in ‘Component Report’.
5. An Example on How to Explore MK4MDD to Generate Hypothesis
MK4MDD will help advance hypothesis-driven research. Here we use an example to demonstrate how MK4MDD will facilitate researchers to generate new hypothesis.
6. Download & Upload
To help user explore the data in MK4MDD, we provided several ways to download and upload data:
- 1) Search result download, including 'Genetic/Epigenetic Locus Search' result download and 'Cross Data Search' result download.
Figure 2 Search result download
- 2) 'My Relationship Set' download and upload.
Figure 3 My Relationship Set download and upload
- 3) 'Download & Upload' module
Figure 4 Batch download and upload search terms or articles to MK4MDD