Freiburg RNA Tools
DiGI - Help
BIF
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Introduction

Given a list of genes known to be associated with a given genetic disease, DiGI predicts and ranks a list of unknown genes based on their probabilities to be related to that disease.

When using DiGI please cite :

Results are computed with DiGI version 1.0.0

Overview

The following parameters are used to control the execution of DiGI

Furthermore, additional information is available

Gene list

?  Gene list to extend

List of disease-associated genes to extend formatted according to HUGO Gene Nomenclature Committee (HGNC)
The parameter constraints are: Number of non-empty entries has to be in range [10,500]. Supported entries can be found in genes-supported-by-DiGI-webserver.txt

Network Decomposition

?  Clique Threshold

The minimum clique size to consider.
The parameter constraints are: Input value has to be parsable as Integer.

?  Degree Threshold

The node degree threshold used for network decomposition procedure. The network achieved after decomposing will have no nodes whose degrees are greater or equal the threshold.
The parameter constraints are: Input value has to be parsable as Integer.

Vectorization

?  Distance

The maximum value for distance parameter of CDNK kernel.
The parameter constraints are: Input value has to be parsable as Integer.

?  Radius

The maximum value for radius parameter of CDNK kernel.
The parameter constraints are: Input value has to be parsable as Integer.

Output Description

DiGI returns a list of genes (not covered by the input) that are ranked in descending order by their predicion to be connected to the genes from input list. That is to be all associated with some disease. By clicking on the gene of interest in the ranking, we are shown i) the sorted neighborhoods regarding the gene in each data source and ii) the information of the gene described in HGNC website. In case, some input genes could not be processed by our tool, they will be listed at the end of the output page.

Input Examples

?  test input

random test input