InteractomeBrowser is a plugin for TranscriptomeBrowser. Its main use is to display networks, given an input list of genes (see video here for quick introduction).
The interactions represented in these networks are mined from several databases (see list below) and are of different natures (proteins belonging to the same complex, kinase-substrate relations, transcriptional regulations, ...).
Currently, InteractomeBrowser integrates the following interaction databases :
- Physical interactions :
- HPRD (v. 9 - 13/04/2010)
- Intact (15/11/2010)
- KEA (2009)
- Regulatory interactions :
- CHEA (06/10/2010)
- LymphTF-DB (02/12/2009)
- OREGANNO (11/2009)
- TFBSConserved (based on hg18 - 17/07/2007)
- TranscriptomeBrowser motif conservation (TBMC, 01/05/2011)
- TargetScan (01/06/2011)
InteractomeBrowser features an original "cell compartments-based layout". It provides a hierarchical representation of cellular compartments, and genes of the network are placed in their respective compartments. When you first select InteractomeBrowser in the plugins list, a settings window will pop up. You will need to choose some options for the current session :
More precisely, we defined an ontology describing cell compartments (with some accurate terms, and some more general terms), which is a subset of GeneOntology:Cell Compartment. The layout is a direct representation of this ontology : small compartments included in bigger compartments correspond to accurate terms that have a "is_a" relationship with another more general term.
- use the compartments-based layout, or not,
- use IEA (Infered from Electronic Assay) annotations from GO, or not,
- which organism you will work on,
- which type of gene IDs you will provide.
Then you can input a list of genes in the left panel, in two ways :
- either by clicking on the "Paste list" button, which will paste the text you previously copied,
- or you can click on "Enter list", which will pop up a dialog with a text area in which you can input your list.
When your list is ready, you can select genes (all of them, or some of them) and click on the "Add >>>" button. InteractomeBrowser will then query the TranscriptomeBrowser database for informations about these genes and their interactions. Then InteractomeBrowser will display the resulting network in the right panel.
The nodes placement is controlled by a force-based layout : the nodes are repulsive to each other, they are attracted to their respective compartments, and edges act like springs. The force-based layout can be switched off or on at any moment through the Display menu. Some parameters of the force-based layout (edge length and edge torsion) can be modified in the same menu.
The network area can be maximized by pressing Alt+F, or by selecting "Full window" in the Display menu.
In order to "clean" the network from orphan nodes and empty compartments, you can select the "Hide orphan nodes" option.
An option called "Hide intercompartmental edges" allows to remove several unlikely edges of the network, when they involve genes belonging to distant compartments.
You can select a gene by clicking on its name (in the list), or clicking on its representing node in the network display. The Edit menu provides several options for selection and removal of genes.
- Interacting with the network
When your mouse is over a node or an edge, you can read information about it, in the "Infos" tab on the left.
Right-clicking on a node will open a context menu, allowing you to :
- open the NCBI web page for this gene,
- add regulatory interactions involving this gene and other genes of the network,
- move the node to another compartment.
The action menu provides other tools to expand the network :
- add all the interactors of the selected genes,
- add common interactors of the selected genes,
InteractomeBrowser also provides an on-the-fly enrichment analysis tool. Select several nodes and click on the "Biological process enrichment analysis" option, and it will pop up a windows with the results of this analysis.
Networks created with InteractomeBrowser can be exported in various formats :
- images (jpg, bmp, gif, png)
- xml format suitable for Cytoscape
- GINML format, to import it in GINsim