PathCards User Guide - What's in a PathCard
Layout
On a desktop browser, the PathCards page is presented in two panes. The larger pane on the right provides the various sections of detailed information as described below. The convenient navigation pane on the left supports easy user-selected examination of the various topics contained in the card.
SuperPathway Name
Each SuperPathway is identified by a textual name derived from one of its constituent pathways, selected as the most connected pathway in the SuperPathway cluster. Selecting this name, as opposed to that of the largest pathway, was chosen since this tends to enhance the descriptive value for the entire SuperPathway. When more than one pathway has the same maximal number of connections, the larger one is chosen as the name of the SuperPathway.
Pathway Network
This section depicts the network of the SuperPath’s pathways. Its named pathway node is shown in the middle of the interactive network widget, with edges leading to the other member pathway nodes. Each pathway is color-coded with the names of its source, as defined in a legend under the network’s figure. The size of each node represents the number of genes within that pathway. The width of each edge corresponds to the number of shared genes between the two pathways connected by the edge.
The figure can be manipulated by directional arrows on the left (on some browsers, navigation provides the opposite of what’s expected), and sizing buttons on the right – especially useful for SuperPaths with a large number of member pathways, such that all of them are not visible without zooming.
Member Pathways
It includes the following sub-sections:
- Pathways - A table of member pathways. The columns contain the Name of the pathway as provided by its linked-to source, the name of that Source, and a list of the Genes in the pathway. Each of these genes is linked to its relevant GeneCard. The first row contains the pathway chosen to provide the name of the SuperPathway as described above. The other rows are sorted by their number of genes.
- Gene overlap in member pathways - Gene overlap in member pathways is displayed as a bar chart. The pathways in the SuperPath, together with a count of their associated genes (in parenthesis), are listed, left-justified, under the chart. Each bar in the chart shows a set of the shared genes (in a mouse-over); under that bar, the member pathways that share all of those genes are marked by a corresponding circle in the relevant pathway rows, to the right of the member pathway name.
Associated Genes
This section includes a table listing information about all of the genes in the SuperPath, ordered by rank (the multiplicity of each gene in the constituent pathways). For each gene, the table’s columns display its Symbol (linked to the relevant GeneCard), Description, Category and the number (#) of Pathways in the SuperPath to which the gene is Related.Associated Disorders
This section includes a table listing information about diseases associated with the SuperPath via the GeneCards Suite’s GeneAnalytics gene set analysis, as documented in the MalaCards Guide’s Data page.
For each associated disease, the table’s columns display the name of the Disease, linked to its MalaCards entry, the Gene symbols, linked to their relevant GeneCards, for all of the SuperPath’s genes that are associated with the disease, and the Score, provided by MalaCards. The rows are sorted by these scores, in descending order.