TargetMine v1.8.5.0 – Data Warehouse for Candidate Gene Prioritisation and Target Discovery

TargetMine v1.8.5.0

:: DESCRIPTION

TargetMine is an integrated data warehouse for retrieval of targetgenes and proteins for experimental characterisation and drug discovery.It utilises a customised InterMine framework, which enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. TargetMine also facilitates analysis of query gene/protein sets for enriched biological themes and associations, which can be employed for candidate gene prioritisation.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

TargetMine

:: MORE INFORMATION

Citation

Chen Y-A, Tripathi LP, Mizuguchi K (2011)
TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery.
PLoS ONE 6(3): e17844. doi:10.1371/journal.pone.0017844

GeneTIER – Expression-based Candidate Gene Prioritisation

GeneTIER

:: DESCRIPTION

GeneTIER replaces the knowledge-based inference traditionally used in candidate disease gene prioritization, instead using experimental data from tissue-specific gene expression datasets.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles.
Antanaviciute A, Daly C, A Crinnion L, F Markham A, M Watson C, T Bonthron D, M Carr I.
Bioinformatics. 2015 Apr 9. pii: btv196.

Endeavour 3.71 – Prioritization of Candidates Genes

Endeavour 3.71

:: DESCRIPTION

Endeavour is a software application for the computational prioritization of candidates genes, based on a set of training genes. It is made up of three stages: training, scoring and fusion. In the first stage, information about the training genes (genes already known to play a role in the process under study) are retrieved from numerous data sources in order to build models. It includes functionnal annotations, protein-protein interactions, regulatory information, expression data, sequence based data and literature mining data. In the second stage, the models are then used to score the candidate genes and to rank them according to their scores. Lastly, the rankings per data source are fused into a global ranking using order statistics. Endeavour is available for human, mouse, rat, fruit fly and worm.

::DEVELOPER

The Bioinformatics Research Group

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

Endeavour

:: MORE INFORMATION

Citation

Tranchevent L., Barriot R., Yu S., Van Vooren S., Van Loo P., Coessens B., Aerts S., De Moor B., Moreau Y.,
“ENDEAVOUR update: a web resource for gene prioritization in multiple species“,
Nucl. Acids Res. (2008) 36 (suppl 2): W377-W384.

Aerts S, Vilain S, Hu S, Tranchevent L-C, Barriot R, et al. (2009)
“Integrating large scale bioinformatics and forward genetics in Drosophila“.
PLoS Genet 5(1): e1000351. doi:10.1371/journal.pgen.1000351