Notice

The screen is composed of two frames: the map area in the center of the screen and the settings area on the left-hand side.

The map area

  1. Description

    The map area contains the diseases and genes relations, presented with nodes and edges.
    The nodes represent diseases. White nodes represent genes. The edges represent correlations between diseases and genes, or relations between diseases if they have a gene in common.
    The size of a node as well as the quantity of edges displayed depend on different parameters found in the settings area (see below). The pale grey zones in the map indicate a high density of links.

  2. Navigating the map with your mouse

    Use your mouse scrolling button to zoom in and out.
    Hold down the left button to move to different areas of the map.

The settings area

  1. Navigation panel

    screencastA navigation panel in the top left hand corner of your screen shows the specific location you are currently viewing inside the map.
    The slider is used to zoom in or out.
    This navigation panel allows you to display the map in two different ways: Classic View (default view) and the Fish Eye View (wide angle view close to 180°).

  2. Size of the nodes

    The size of a disease node is either determined by its Hub Degree

    Hub Degree:
    The size of a node is proportional to the number of outbound links. The more outbound links there are, the bigger the node is.

  3. Categories and Colors

    screencastEach disease category has been assigned a specific color, displayed close to its name.
    The “Hide All” and “Show All” buttons allow to display or hide all the nodes on the map. Clicking on a category will display or hide all this category’s nodes.

  4. Distribution panel

    screencastThe distribution of the different categories on the map can be seen as a pie chart or a bar chart. They help you to see the part of each category, due to the number of their elements.
    Roll over the various segments of the charts to have more details on each category (number of nodes, percentage of the total number of diseases on the map).

  5. Disease or gene panel

    screencastWhen a disease or a gene is selected, all the links to and from it are shown
    Category of the selected disease is available in the settings area.

  6. Search panel

    screencastIt is possible to search for a specific disease or gene on the map, based on its name in full or in part.
    You can restrict the search to a specific category.
    The results will be displayed at the bottom of the search panel.

  7. Links panel

    screencastBy default, only disease-disease edges on the map are displayed. Select all visible links to display disease-gene edges.
    In darkgrey are displayed simple links (from a site A to a site B) and in lightgrey mutual links (when sites A and B link back and forth to each other).

    3 different colors show the nature of the links for selected nodes: inbound links to a gene are red, outbound links from a disease are yellow, and mutual links between two diseases are green.

    If your computer is powerful, you may choose the antialiased render.

    The maximal links size slider enables the displaying of links based on their lengths between two nodes.

Hints

Curious about the Diseasome map? Here are some answers to the most common questions asked:

I. Drawing the map

The Diseasome map is composed of 516 diseases and 903 genes - using the data of Marc Vidal, Albert-Laszlo Barabasi and Michael Cusick.

The diseases are divided into twenty-two different categories:

  • Bone
  • Cancer
  • Cardiovascular
  • Connective tissue disorder
  • Dermatological
  • Developmental
  • Ear,Nose,Throat
  • Endocrine
  • Gastrointestinal
  • Hematological
  • Immunological
  • Metabolic
  • Muscular
  • Neurological
  • Nutritional
  • Ophthamological
  • Psychiatric
  • Renal
  • Respiratory
  • Skeletal
  • Multiple
  • Unclassified

II. Navigating the map

The Diseasome map’s default view is set to display all the categories and genes at once. You can select the individual categories you’re interested in and more carefully analyze the links existing between them and the genes.See the notice for more practical details on map navigation.

III. Understanding the map

As shown in the map’s navigation bar, a node’s color indicates the category it belongs to, and a disease node’s size indicates its hub degree (overall number of outbound links).

The more links a node send to gene nodes shown on the map, the bigger it appears on the map.

Nodes are positioned on the map according to a topological placement algorithm, i.e. each node is positioned solely according to its linking pattern. Many softwares are available for doing this. Gephi has been chosen for its high quality algorithm ForceAtlas.

Many algorithms make possible for a 2D rendering of an adjacent matrix - i.e. the matrix describing any graph. We used a ForceAtlas algorithm, which shares with all the others the same basic principle: minimizing the system’s energy while maximizing the use of the space available for the representation of the data. To minimize the system’s energy, one can for instance assume that nodes that are not linked to each other are pushing away from each other whereas nodes that are linked to each other are attracting each other. Through iterative steps the algorithm tries to find a way to position nodes where there is as little link overlap as possible. To maximize the use of the mapped space, the graph is spread as much as possible over the surface allocated for its display.

These positioning principles call for the following reading conventions:

  • A node’s position on the map depends solely upon its links. A node has no predefined position, the latter being the result of the relations it has with other nodes. This means that a node with no links at all cannot be positioned on the map;
  • North, East, South and West don’t matter. The displayed space is not based on the cardinal system (North, East, South, West), which means that the choice of a relative left-right or top-down position is purely arbitrary;

That’s it. Now you can navigate inside the Diseasome map and analyze in detail the relations between diseases and genes.