Resources
Resources

GNF provides public access to results from some of its most significant tools and discovery projects. We also use our own custom-built databases and applications to publish unique large-scale datasets on gene function and genetic polymorphism such that their value to the scientific community is maximized. This page provides an overview of tools currently available on our web site, along with a brief summary.

BioGPS. This popular gene annotation portal provides convenient access to hundreds of online gene annotation databases [1]. Instead of searching through gene annotation sites individually, users can access any of these sites through the unified BioGPS interface. BioGPS emphasizes community extensibility by allowing any user to add to our extensive plugin library through our simple and lightweight plugin interface. BioGPS also stresses user customizability, allowing each user to personalize which gene annotation resources are relevant for them.

P. falciparum e-Annotation Database. Ontology-based Pattern Identification (OPI) is a novel data-mining algorithm that systematically identifies gene/protein expression patterns that best represent existing knowledge of gene function [4]. We applied OPI to a gene expression data set (publicly available) on the life cycle of the malarial parasite P. falciparum and systematically annotated genes for several hundred functional categories. The database provides a systems-wide biological view of the parasite.

Redundant siRNA Activity (RSA) Analysis Tool.  RSA is a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference screens in mammalian cells.  Application of this analysis significantly enhances reconfirmation rate [5].

We make extensive use of Open Source software packages in our in-house built informatics systems, and we have also contributed back to the community substantially.

  1. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009;10(11):R130. 
  2. Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, et al. Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol 2004;2(12):e393. 
  3. Orth AP, Batalov S, Perrone M, Chanda SK. The promise of genomics to identify novel therapeutic targets. Expert Opin Ther Targets 2004;8(6):587-96. 
  4. Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, Winzeler EA. In silico gene function prediction using ontology-based pattern identification. Bioinformatics 2005;21(7):1237-45. 
  5. Konig R, Chiang CY, Tu BP, Yan SF, DeJesus PD, Romero A, Bergauer T, Orth A, Krueger U, Zhou Y, et al. A probability-based approach for the analysis of large-scale RNAi screens. Nat Methods 2007;4(10):847-9.