Graph Display Options
contains two main
sections, which can be opened by selecting the corresponding tab:
1. Edge Filter – provides a brief description and some useful links about a particular gene in the graph.
2. Node Attribute – select node attributes to be highlighted on the graph.
Edge Filter (TOP)
Edge Filter Panel provides a
menu of the different
functional edge types available. This menu is constructed automatically
from stored data types
and/or data uploaded by the user
(see " Uploading Data").
Mouse-over data descriptions
Mousing over each menu item (i.e. edge type or dataset) will cause detailed information for that item to be displayed.
Changing edge colors
Each edge type defaults to a color chosen by the system. Colors can be easily changed by the user by clicking on one of the colored boxes on the left of the menu and selecting a new color from the palette.
Filtering by number of edges
Users can choose to display all links between nodes or only those links that are supported by multiple independent pieces of evidence. This is controlled by the "Multi-Edge Only" checkbox at the top of the Edge Filter Panel. If selected, then it shows only multiply supported links. Selecting this option hides from view all links between nodes that are only supported by a single piece of evidence. The remaining "multi-support" links may be supported by two or more different edge types (e.g. protein interaction and genetic interaction) AND/OR by edges from two or more datasets of the same type .
If unselected, then show all edges for selected types and datasets(normal).
Users can also choose to display only links between the query nodes. This is controlled by the "Spoke View Only" checkbox at the top of the Edge Filter Panel. If selected, then it shows only the nodes and edges connected to the query nodes. If unselected, then all interactions between nodes are displayed.
Users can also select both "Multi-Edge Only" and Spoke View Only" checkboxes to view multiply connected links between nodes that are only connected to the query nodes.
datasets and numerical thresholds
By default, all data types and data sets available are included for display. This can result in a very large number of edges being included in the display. Users can limit the edges displayed using check boxes for different data types and datasets, and by changing the numerical cutoffs (where present). The Edge Filter allows one to toggle the display of edges between hidden and visible.
Clicking on the button with "..." on the right of the datasets brings up a window that allows one to choose Small, Medium, or Large for the size of edges for that dataset.
Clicking on the double arrows expands/collapses the display of the datasets for a type.
Node Attribute (TOP)
Paints selected attributes on nodes in the current graph. Any node "attributes", such as phenotypes, sequence conservation, protein domains, etc. available can be painted on the network graph in the Graph Display Panel. Like the Edge Filter, the Node Attribute menu is auto-generated from data in the N-Browse database.
Selecting Attributes for Display
When the Node Attribute tab is opened, a list of
available attributes will be displayed (for example, phenotypes,
protein domains, etc.). Select a checkbox to load the corresponding
attribute class for highlighting on the graph.
Node attributes may be highlighted with either a graded scale of color intensity (for numerical data) or a solid color (for categorical data).
Type 1: Color Scale (Rainbow)
Attributes with a numerical range may be displayed with either a regular numerical scale or a log scale. All nodes in the current graph with a numerical value for this attribute type will be painted according to the color scale. Nodes with no value will become gray.
Example: BLAST e-values between two species, such as "Ce_Dm BLAST e-value" available for C. elegans.
Type 2: Category and Range Value
Search the graph by category.
Example: Phenotypes with penetrance values, available for C. elegans. "Emb" will select genes with embryonic lethality.
The collection of nodes in the current graph can be searched for attributes individually, or in combinations of two or more using the logical operators AND ("&") and OR ("|"). (Note: the OR operator has higher precedence than the AND operator).
The current combinatorial search function allows only a limited range of combinations but will be expanded in future versions.
Term1 => Highlight genes in the current graph whose attributes contain Term1.
Term1; Term2;& => Highlight genes in the current graph whose attributes contain "Term1 AND Term2".
Term1; Term2; | => Highlight genes in the current graph whose attributes contain "Term1 OR Term2".
Term1; Term2; Term3; & => Highlight genes in the current graph whose attributes contain "Term1, Term2, AND Term3".
Term1; Term2; &; Term3; | => Highlight genes in the current graph whose attributes contain "(Term1 AND Term2) OR Term3".