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:
- select 2 random edges
(a,b)
and (c,d)
so that a != b != c != d
- delete the original edges and insert two new edges
(a,d)
and (c,b)
- 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:
- pool baits (default): one purification experiment for each bait with all of its baits is created
- 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.
- Enter comma-seperated lists of protein IDs into the text fields
"Proteins 1" and "Proteins 2", or leave them empty to show all proteins
- For directed networks, "Proteins 1" will filter the edge sources where as "Proteins 2" filters the targets of each the directed edges
- In the "Filter" text field you can enter boolean expressions,
only edges whose annotations match this expression will be shown in the
result. The edge weight is also treated as an annotation with the name
@weight
. See also: Annotations
and filtering
- Press [Enter] anywhere in the text fields to start your query.
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:
- A diagram containing the number pairs described above.
- The correlation coefficent between these two rows of data (Pearson or Spearman).
- A file containing the comparison data