This guide is to help you with navigating the content of the map, searching for drug targets and visualising publicly avalilable datasets or your own data.
User manual#
The PD map is hosted on the MINERVA Platform for online access and exploration. Detailed user manual is available on the MINERVA website, describing how to browse the content, visualise data, and use the map as a computational resource. You can also check tutorial videos available there.
Below is a short summary of functionalities of the PD map.
Getting started#
The Parkinson’s disease (PD) map (https://pdmap.uni.lu)
- displays disease-related molecular and biochemical pathways within a neuronal cell system, focused on a dopaminergic neuron, adjacent cells (i.e., astrocytes, microglia) and cellular structures (i.e., blood-brain-barrier, synaptic terminals).
- has an intuitive display enabling easy navigation.
Structured view is the default view providing, where details are revealed as you zoom in.
Network view shows a detailed diagram.
Submaps
- Contents of the PD map are split into pathway diagrams, describing specific mechanisms.
- Search functions and data display works simultaneously on the whole PD map and on the submaps.
How to browse and search#
Browse
- An intuitive “Google Maps” display enables easy navigation through the PD map
- Clicking any element in the PD map (e.g., proteins, molecules or phenotypes) provides detailed annotations and links to external databases
- Clicking on an interaction between elements provides information on reactants and links to the underlying sources (i.e., PubMed, Reactome or KEGG)
- Project info gives you information about the map, and the link to the list of the current publications curated into the PD map (Publications)
Search
- All elements of the map are searchable
- Search for multiple elements: separate terms by a semicolon
- “perfect match” toggles a strict search
- Search results are visible on the map and in the left panel
- You can find specific elements using keywords
- Search for reactions: use reaction:[rid], where [rid] is a reaction identifier in the map
- Search for publications and related interactions: use pubmed:[pmid], where [pmid] is the PubMed ID
Search for drug or small molecule targets
- Use the same search field to look for drug or small molecule targets in the map
- Potential targets are fetched from the drug databases DrugBank and ChEMBL, displayed and marked in the PD map
- Additional information concerning the drugs and the potential targets, including links to drug databases and PubMed is provided in the left panel
How to visualise data#
- Overlays button shows datasets that can be visualised in the PD map.
- Shared overlays are publicly available datasets, including
- Ageing brain: Differentially expressed genes in healthy aging brain, kindly provided by Enrico Glaab, see: Glaab and Schneider, 2015.
- PD substantia nigra: Differentially expressed genes in PD substantia nigra, kindly provided by Enrico Glaab, see: Fujita et al., 2013.
- When visualising data, the map is show in black and white for better display
- Multiple datasets can be displayed at the same time
- Multi-coloured elements are links to underlying pathways, and show a summary expression of the underlying diagram
- Click on an element to see detailed information in the left panel
Uploading your data#
To visualise your data in the map, you need to log in first.
Use your ORCID credentials, or contact us (marek.ostaszewski@uni.lu) for an account.
When logged in:
- Click on Add overlays
- Either
- Upload an overlay file (see below)
- Provide list of element names (one per line)
- Name the overlay and assign in to a group (‘Without group’ is the default one)
- Click Upload
- The new file will appear in the User provided overlays section
Upload of a data file: Data preparation
- Data file needs to be uploaded as a .txt file that consists of two columns
- name - names of elements to be visualised, as they appear in the map
Note: data from other species than human, the species-specific identifiers need to be translated to human identifiers - value - contains values between -1 and 1
Note: because values are directly transformed to a colour range, dataset values need to be normalized into [-1,1] range
- name - names of elements to be visualised, as they appear in the map
Please note:
- You can combine display of “Shared overlays” and your data
- Contact us (marek.ostaszewski@uni.lu) if you need any help with visualising your data on the map
- All uploaded data are accessible by the system administrators due to technical reasons but they are not visible by any other user.