Complex sets menu

Contains methods to manipulate, display and evaluate complex sets.

Overview

Load set from file

Loads a complex set from a user-specified file.

See also: File formats

Save set to file

Saves a complex set to a user-specified 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 set

Assigns a new internal name for the selected complex set.

Dispose set

Deletes the complex set from the complexes list. Note: This will not affect an eventual file the set was loaded from.

Show complexes and scores

Opens a window which lets you investigate the complexes in the selected set as well as complex scores with respect to a given scores network.

Show complex size histogram

Displays a histogram of the complex sizes in the currently selected dataset.

Comparison

This submenu contains two methods to compare complex sets with each other.

Brohee comparison

Calculates sensitivity, positive-preditive value and accuracy according to Brohee et al., 2006. You can select more than two complex sets, ProCope will perform an all-against-all comparison.

See also: Complex set evaluation

Map complexes

This method attempts to map complexes between two selected complex sets. For all methods except Exact mapping the user has to choose an overlap threshold needed for two complexes to be mappable (default: 2 proteins). The user can select 4 ways to perform this mapping process.
  1. Only one mapping per complex - Each complex can only be mapped once. If there are multiple overlaps with complexes in the other set, the one with the largest overlap will be the mapping partner.
  2. Multiple mappings per complex - Each complex will be mapped to all complexes in the other set for which the protein overlap is large enough.
  3. Unambigous mapping - A complex is only mapped if it has only one mapping candidate in the other complex set
  4. Exact mapping (identical complexes) - Finds identical complexes between the two complex sets.
See also: Complex set evaluation

Quality

This submenu contains methods to evaluate the quality of a complex set based on colocalization data or GO annotations.

Colocalization

Evaluates the degree of colocalization of all complexes in the selected set.

See also:

Semantic similarity (GO)

Evaluates functional similarities of the members of each complex in the selected set.

Important note: The protein identifier types used in the GO files might not be the same as in the other data files. You might have to use a name mapping file. ProCope provides such a name mapping file for yeast in data/yeastmappings_YYMMDD.txt.

See also:

Manipulate

The "Manipulate" submenu contains methods for restricting, filtering and processing the selected complex set.

Size cutoff

Deletes all complexes which have more or less than a given number of proteins.

Score cutoff

Deletes all complexes whose average complex score with respect to a given network is below a certain threshold. When Ignore missing scores is enabled, protein-protein interactions in the complex which have no edge in the network are not scored 0 but ignored.

Restrict to proteins

Retains only those complexes in the set whose members are in a given protein set. The user can choose whether all proteins of the complex have to be contained in this set or if just one member of the complex is sufficient. The 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).

Decompose

Treats each complex as a graph where the edge weights are taken from a given scores network. All edges below a given threshold are deleted and thus the graph may decompose into two or more subgraphs. These subgraphs create the resulting complex set of decomposition.

Add shared proteins

Adds shared proteins to the complex sets. You can choose between the method described in the publication of our bootstrap approach or the method by Pu et. al.

See also: Complex set prediction

Randomize

Contains two methods to randomize the seleted complex set(s).

by exchanging

Exchanges proteins randomly between complexes. The size of the complexes as well as the number of complexes a protein is contained in will be preserved.

by remapping

Randomization is achieved using a random permutation of the proteins. That means, for instance, that all occurences of Protein1 will be replaced by Protein4, all occurences of Protein2 will be replaced by Protein3 and so on. The sizes of the complexes will be preserved.

Get complex-induced network

Returns a network containing an edge for each pair of proteins which are in the sample complex. All edges have a weight of 1.0.


ProCope documentation