GenoScape is a Cytoscape plugin (http://www.cytoscape.org) originally designed for GenoScript users (http://genoscript.pasteur.fr). GenoScape enables the visualisation of expression data, either stored in GenoScript or loaded from files, and mapped onto KEGG pathways.
GenoScape has been published in Bioinfomatics in 2009.
If your using GenoScape plugin, please cite it as :
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. M.Clement-Ziza; C.Malabat; C.Weber; I.Moszer; T.Aittokallio; C.Letondal; S.Rousseau. Bioinformatics 2009; doi: 10.1093/bioinformatics/btp464
Free-access links to the online article:
PDF:
http://bioinformatics.oxfordjournals.org/cgi/reprint/btp464?ijkey=qFlscjhPmirWAcw&keytype=ref
http://www.cytoscape.org/
GenoScape has been tested with Cytoscape release 2.6 on Macintosh and Windows
systems.
Note for Macintosh developers: the application will not work if cytoscape.jar is in the /Library/Java/Extension/ directory.
Place genoscape.jar in the plugins directory of the Cytoscape installation directory.
The plugin is automatically loaded when Cytoscape is launched.
If you are using a proxy, you have to configure the proxy server in Cytoscape by going to Edit > Preferences > Proxy Server:
This setting will be applicable during the current session only. To set the proxy permanently, go to Edit > Preferences > Properties, selectMake current Cytoscape properties default and click on Ok.
If the GenoScape plugin is installed properly, it should be automatically loaded in Cystocape at launch time.
A new item called “Genoscape” is now visible in the main menu bar:
The online documentation is accessible from the Genoscape entry of the Help menu:
GenoScape enables the mapping between expression values and a biological network. In the current version, only KEGG pathways are supported networks. Expression values can be directly imported from the GenoScript database (Browse GenoScript menu) or uploaded from files (Import from file menu).
KEGG pathways are downloaded from the KEGG repository and converted into GenoScape specific tab-separated files. Depending on your network connection, importing KEGG pathways may be a time-consuming process. In our hands, a typical download lasts about 10 minutes for a bacterial pathway. Upon download, tab-separated files are stored in a directory named following the KEGG organism code (usually a 3-letter code). This directory is automatically created for each organism, and is located in the dbFile sub-directory of the Cytoscape plugins directory. Tab-separated file names contain the KEGG pathway accession number they are related to. Permanent storage of pathway files saves you from downloading these data repeatedly when using GenoScape: they are downloaded only once for each organism.
You can use public experiments, or access your (private) experiments by entering your login and password:
The experiment list is organised as follows:
One or several analysis may be available for each experiment. Each analysis contains at least one dataset. For example, if we consider a time series experiment with 3 time points: time0, time1 and time2, we can compare time1 vs. time0 and time2 vs. time0 in the same analysis process. These 2 comparisons correspond to 2 datasets.
The GenoScape plugin can handle several datasets at the same time. You can choose a single dataset or select "All Data Sets".
Gene accession number |
Log-Ratio |
Significant |
Description |
… |
lpl1229 |
-2.34 |
1.0 |
Fagellar biosynthesis protein |
… |
lpl1653 |
1.10 |
0.0 |
Aconitate hydratase |
… |
…. |
GenoScape uses a tab-separated file format. The first three columns (in red in the example above) are mandatory:
Column |
Name |
Content |
1 |
Gene accession number |
Same accession number as KEGG |
2 |
Log-ratio |
Log-ratio expression value or any other value This value is used to define the color of the nodes |
3 |
Significant |
1
if the gene is significantly regulated |
Other columns are also imported in Cytoscape |
||
Column names are not constrained: you can assign any name. However, column order must be respected.
If you do not want to provide “Significant” values, leave the column empty.
Upon import, mandatory columns are renamed:
• Column
1 => Id
• Column 2 => logRatio
• Column 3 => Significance
GenoScape retrieves the organism studied in the experiment, and either imports the corresponding networks from the hard drive, or downloads them from the KEGG repository (should if you work with this organism for the first time).
Loaded networks are listed in the left-hand panel (Control Panel). The first network in the list stores all the nodes and edges of the experiment loaded by the user. In the Figure below, this network is highlighted in green, indicating that it is open in a Cytoscape view:
No view is created for the other networks: their large number could overload the memory buffer. Networks with no view are highlighted in red. After the complete loading of the networks, right-click on a network name and select Create View to display this network:
In the Control Panel, some pathways may be absent if GenoScape could not find any match between experiment nodes and pathway nodes.
If needed, only a part of the networks can be imported. To this end, open the file “pathway_[org]” (org is the 3-letter code for organisms in KEGG) in the directory {cytoscapeDir}/pulgins/dbFile/[org]:
To omit a pathway during import, you should just change the value in the second column from “Display” to “Hide”:
Then, save and close the file. Only the pathways with the “Display” option value will be imported during the next session of GenoScape.
The network nodes are initially organized in a Grid layout (nodes are arranged following a square grid). You can also use more convenient visualisation styles using the Layout menu. We recommend the Layout > yFiles > Organic layout and the Layout > yFiles > Circular layout.
A Genoscape visual style is created and added to the VizMapper visual style list.
This visual style can handle node color, node label, node label opacity, node line width, node opacity, node shape, edge color and edge line style.
Nodes symbolise proteins and genes.
Node attribute |
Example |
Default value from … |
Notes |
||||||
Label |
|
genoscape.label |
|||||||
Shape |
|
genoscape.type |
Gene -> round shape Undefined -> square shape (default) |
||||||
Opacity, |
|
genoscape.type |
Gene -> full opacity (default) Ortholog -> 10 % opacity |
||||||
Color |
|
logRatio |
It uses the VizMapper continuous mapping option with the following color scale:
Grey nodes corresponds to genes with no associated expression value |
||||||
Size |
|
Significant |
0 -> size 35 (default) 1 -> size 50 |
||||||
Nodes are linked together by edges when there is a relationship between cognate genes in the KEGG pathway.
|
Edge color and style depend on the interaction edge attribute: pp -> solid black line pd -> red dashed line |
Attribute |
Description |
NODES |
|
Expression values |
|
[data set].FDRpvalue |
FDR p-value of the signal, as given in GenoScript. Corrected p-value based on a False Discovery Rate method (e.g. Benjamini and Yekutieli) |
[data set].FWERpvalue |
FWER p-value of the signal, as given in GenoScript. Corrected p-value based on a FamilyWise Error Rate method (e.g. Bonferroni) |
[data set].logRatio |
Log of the ratio Cy5/Cy3, as given in GenoScript or in an imported file |
[data set].rawpvalue |
Raw p-value of the signal, as given in GenoScript |
[data set].Significance |
Significance of the expression value, as given in GenoScript or in an imported file |
Label |
|
Genoscape.label |
Label of the node displayed in networks. The label is the gene_symbol if it is available, the accession number otherwise |
Name and accession number from KEGG |
|
Genoscape.accession_number |
Accession number of the node in KEGG |
Genoscape.gene_symbol |
Gene name of the node in KEGG |
Genoscape.type |
Type of the node as described in KEGG |
Name and accession number from GenoScript |
|
Gene_name |
Gene name (symbol) |
Gene_accnum |
Gene unique accession number |
Gene_descript |
Gene description |
Probe_name |
DNA chip reporter name |
Cross-references |
|
Genoscape.ec |
EC number of the node in KEGG |
Genoscape.jcvi-cmr |
Entry name of the node from the J. Craig Venter Institute |
Genoscape.ncbi-geneid |
Gene ID of the node at NCBI |
Genoscape.ncbi-gi |
Protein ID of the node at NCBI |
Genoscape.pasteur |
Entry name of the node at Institut Pasteur |
Genoscape.pasteur-lpf |
Specific name of the node at Institut Pasteur |
… |
Other attributes can be found depending on the organism studied, as KEGG provides database entries specific to each organism |
Others |
|
Source |
Source of the data |
EDGES |
|
Interaction |
Type of relation: pd: genes belonging to the same KEGG Orthology group (same “KO” identifier) pp: genes having a “relation” as defined in KEGG pathways |
