Using predictive specificity to determine when gene set analysis is biologically meaningful

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets

(2014) Kimberly Glass et al.   Scientific Reports

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences

(2013) Elodie Portales-Casamar et al.   BMC GENOMICS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

GO-Elite: a flexible solution for pathway and ontology over-representation

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

Down-weighting overlapping genes improves gene set analysis

(2012) Adi Tarca et al.   BMC BIOINFORMATICS

An environmental analysis of genes associated with schizophrenia: hypoxia and vascular factors as interacting elements in the neurodevelopmental model

(2012) R Schmidt-Kastner et al.   MOLECULAR PSYCHIATRY

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns

(2011) Xinan Yang et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders

(2011) Dan Levy et al.   NEURON

Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses

(2011) Sarah R. Gilman et al.   NEURON

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Identifying informative subsets of the Gene Ontology with information bottleneck methods

(2010) Bo Jin et al.   BIOINFORMATICS

The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems

(2010) Nophar Geifman et al.   BMC BIOINFORMATICS

Automatic, context-specific generation of Gene Ontology slims

(2010) Melissa J Davis et al.   BMC BIOINFORMATICS

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

(2010) Mercedes Pardo et al.   Cell Stem Cell

Gene function analysis in complex data sets using ErmineJ

(2010) Jesse Gillis et al.   Nature Protocols

Entrez Gene: gene-centered information at NCBI

(2010) D. Maglott et al.   NUCLEIC ACIDS RESEARCH

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

A probabilistic generative model for GO enrichment analysis

(2008) Yong Lu et al.   NUCLEIC ACIDS RESEARCH