AGRA: analysis of gene ranking algorithms.

Bioinformatics 2011 Apr 23;27(8):1185-6. Epub 2011 Feb 23.

Faculty of Health Sciences, University of Maribor, Maribor, Slovenia.

Unlabelled: Often, the most informative genes have to be selected from different gene sets and several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the analysis of gene ranking algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system finding-associated concepts with text analysis. AGRA defines what we call biomedical concept space (BCS) for each gene list and offers a comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where a specific biomedical concept can be entered. AGRA searches for this concept in each gene lists' BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it.

Availability And Implementation: Available at http://agra.fzv.uni-mb.si/, implemented in Java and running on the Glassfish server.

Contact: simon.kocbek@uni-mb.si.

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072556PMC
April 2011
5 Reads

Publication Analysis

Top Keywords

ranking algorithms
16
gene ranking
16
gene lists
12
gene
10
biomedical concept
8
analysis gene
8
agra
5
bcs categories
4
offers comparison
4
comparison gene
4
categories uploaded
4
lists bcs
4
compared methods
4
overlap pair
4
pair gene
4
lists bcss
4
method overlap
4
methods method
4
lists compared
4
list offers
4

References

(Supplied by CrossRef)

Jelier et al.
Genome biology 2008

Bioinformatics 2004

Ma et al.
BMC bioinformatics [electronic resource] 2006

Maier et al.
Nucleic Acids Research 2005

DRUGS TODAY 2002

Mailund et al.
BMC bioinformatics [electronic resource] 2006

Bioinformatics 2008

Similar Publications