Start
The typical analysis steps are:
Choose genome
(Currently available organisms:arabidopsis thaliana, bacillus subtilis, helicobacter pylori, listeria monocytogenes, listeria innocua, thermoplasma acidophilum, saccharomyces cerevisiae,neurospora crassa
)
Select the knowledge modules that should be used for bias evaluation
Upload the gene network structure
Upload user defined knowledge modules (if any)
Start the computations
Attention!!
Before using BIOREL you should convert the geneIDs of your network into the geneIDs employed by FunCat database.
For each organism the gene names can be mapped using the Map files
(
arabidopsis thaliana ,
bacillus subtilis ,
helicobacter pylori ,
listeria monocytogenes,
listeria innocua,
thermoplasma acidophilum,
saccharomyces cerevisiae,
neurospora crassa,
).
The gene names other than FunCat will be ignored.
Network format
The network should be specified in a file.
The lines specify the network edges.
Each line starts with two gene names (required information).
The last numeric value in a line indicates the edge weight (optional).
All values are separated by comma.
If the information for the edge weight is absent then the default value of edge weight is 1.
The edges that are not specified in a file considered to have zero weight.
The example below specifies the network of 5 genes with 6 edges:
YER175C,YLR158C,1
YER175C,YHR178W,0.5
YER175C,YGR129W,0.75
YGR129W,YDR416W,2
YER175C,YDR416W,0.75
YDR416W,YLR158C,0.5
User Knowledge Module format
The user can upload his own Knowledge modules (up to 4 files) in a network format.
This module can be used together with a standard system modules (FunCat, SS, IPD,PPI) to estimate the target network biological relevance.
The format of the file is Network format.
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BIOREL
