Chronic Neuroinflammation Mechanisms Map

Online access and exploration: https://pathwaylab.elixir-luxembourg.org
Development status: Available for exploration online
Diseases: Alzheimer’s disease, Parkinson’s disease, multiple sclerosis
Sustainable support: LCSB, MINERVA Platform
Construction tool: CellDesigner
License: Creative Commons Attribution 4.0 International (CC BY 4.0) License
Publication: Manuscript in preparation
Contact: Oxana Lopata, University of Luxembourg, oxana.lopata@uni.lu

Description

The map is accessible here. It reflects what is currently known of inflammatory mechanisms in the central and peripheral nervous system, focusing on pathologies of Alzheimer’s disease (AD), Parkinson’s disease (PD), Multiple Sclerosis (MS), and similar conditions. The map provides standardised, detailed, diagrammatic pathway-level description of persistent activation of the brain’s immune system, leading to long-term inflammatory signaling.

The resource is hierarchically structured as a multilayer network of submaps, representing a collection of biological processes and pathway modules across neurodegenerative diseases, describing disease mechanisms at different layers of granularity, with a focus on common components of chronic inflammation.

User guide

The main entry point to the map is available here. This is a top-level overview diagram representing main general aspects of chronic neuroinflammation.

Pan and zoom

Zooming and navigating for browsing the map content are similar to working with Google Maps. It is also possible to use the buttons on the lower right corner to zoom in, zoom out and center the map content.

Interactive exploration

To access information about map elements - cell types, phenotypes, proteins, genes, interactions - please click on the element and check the appearing panel with the description on the left.

By clicking on a map interaction (black lines that connect map elements) you can access references to publications supporting this reaction.

Search

You can search for elements using the search panel and see them highlighted with anchors on the main map. In the left panel, under the Contents section, you will see which submaps contain detailed mechanisms. To clear the search, please use the Clear button.

Submaps

To access the pathway specific maps, please click the Submaps button above. You will see the list of the submaps in the left panel. By clicking on the Open button near the submap name you will be accessing the corresponding submap.

Here you can also search for elements, check description and references etc.

Data visualisation

To visualise experimental dataset on the map, please use the Overlays button above.

The left panel will display the list of integrated datasets. Click View to visualise an overlay of interest.

The elements present in selected overlays containing datasets with differential expressed genes or proteins along with their normalized LFC values are highlighted in a gradient color according to their normalized LFC values as shown in the horizontal bar at the bottom of the panel Overalys. Several datasets can be shown at the same time.

To remove the highlights, please click Hide.

Acknowledgements

This project is supported by ELIXIR Luxembourg (ELIXIR-LU) Node. ELIXIR-LU hosts and maintains the MINERVA Platform for this project and supports its development.