Networks menu

This menu contains methods to analyze, manipulate and query protein interaction networks.

Overview

Load network from file

Loads a protein interaction network from a given file. The user will be asked whether this network shall be loaded as a directed network. When loading a directed network, the first protein of each edge is used as the edge's source, whereas the second protein is the target of the directed edge.

Both edge weights and eventual edge annotations will be loaded from the file. GZIPed files are automatically detected and decompressed.

See also: File formats

Save network to file

Saves a network to a user-selected file. Both edge weights (scores) and annotations will be saved. Use the "Save data objects GZIPed" option to store the network in a compressed file.

See also: File formats

Export to Cytoscape

Exports a Cytoscape-compatible XGMML file or directly creates a new graph within Cytoscape when running in plugin mode.

See also: Cytoscape integration

Rename network

Assigns a new internal name for the selected network.

Dispose network

Deletes the network from the networks list. Note: This will not affect an eventual file the network was loaded from.

Quality

This sub-menu contains methods to evaluate the quality of a scrores network with respect to a reference protein complex set.

Complex enrichment

Calculates the complex enrichment value of the selected networks. By default, the program will perform 100 randomizations of the reference complex set to minimize variations.

See also: Network evaluation

ROC

Calculates ROC curves for the selected networks.

See also: Network evaluation

Manipulate

This sub-menu contains methods to manipulate the selected score network. 

Cut-off network

This function will delete all edges from a network whose weight is below a given threshold value.

Filter network

Filters the network by only retaining edges in the network which match a given boolean expression. The edge weight is also treaded as an annotation with the name @weight.

See also: Annotations and filtering

Restrict to proteins

Retains only those edges in the network where one or both associated nodes are in a given set of proteins. This restriction set may come from another data object (network, complex set, purification dataset), from the user directly or from a filtererd subset of annotated proteins (see also: Protein annotations).

Scalar multiplication

Multiplies all edge weights of the network with a scalar factor. Edges which have an annotation but no weight are ignored.

Randomize

Randomizes a network by rewiring. The rewiring process works as follows:
  1. select 2 random edges (a,b) and (c,d) so that a != b != c != d
  2. delete the original edges and insert two new edges (a,d) and (c,b)
  3. repeat a given number of iterations
Both edge weights and annotations (i.e. the full edge) is a affected by rewiring. The default and recommended number of iterations to get a good randomized result is 10 times the number of edges in the network.

Derive purification data

Converts a directed network into a purification data set. For each directed edge a => b, a is used as the bait of a purification and b as its prey. There are two different approaches of creating a purification data set from the resulting set of bait-prey interactions:
  1. pool baits (default): one purification experiment for each bait with all of its baits is created
  2. do not pool baits: a single experiment for each bait-prey interaction is created (warning: might result in large purification data sets)

Merge

Merges two networks into one. Different settings which control the merging process can be specified. See also: Networks

Cluster

Clusters a network using one of the built-in clustering algorithms or a user-defined algorithm. Produces a complex set (= clustering) as its output.

See also:

Query tool

Opens a new window containing a small tool to show edges from the selected network.

Histogram

Shows a histogram of any numeric annotation present in the network. Choose @weight from the annotation list to use the edge weights.

Compare

Compares edge weights of the two selected networks. The function generates a list of number pairs (x,y) containing the weights of a given edge from both networks. If an edge is only present in one network, a weight of 0 will be assumed for the other network. Three types of output can be produced:




ProCope documentation