Visual annotation display (VLAD): a tool for finding functional themes in lists of genes

[1]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[2]  Judith A. Blake,et al.  The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease , 2014, Nucleic Acids Res..

[3]  Kimberly Glass,et al.  Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets , 2012, Scientific Reports.

[4]  Jing Wang,et al.  WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 , 2013, Nucleic Acids Res..

[5]  Cynthia L. Smith,et al.  The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data , 2012, Mammalian Genome.

[6]  C. Bult,et al.  Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes , 2012, Proceedings of the National Academy of Sciences.

[7]  Peter N. Robinson,et al.  GOing Bayesian: model-based gene set analysis of genome-scale data , 2010, Nucleic acids research.

[8]  William Stafford Noble,et al.  How does multiple testing correction work? , 2009, Nature Biotechnology.

[9]  Carol J Bult,et al.  MouseCyc: a curated biochemical pathways database for the laboratory mouse , 2009, Genome Biology.

[10]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[11]  Peter J. Woolf,et al.  GAGE: generally applicable gene set enrichment for pathway analysis , 2009, BMC Bioinformatics.

[12]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[13]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[14]  Erhard Rahm,et al.  FUNC: a package for detecting significant associations between gene sets and ontological annotations , 2007, BMC Bioinformatics.

[15]  Ziv Bar-Joseph,et al.  STEM: a tool for the analysis of short time series gene expression data , 2006, BMC Bioinformatics.

[16]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[18]  Seon-Young Kim,et al.  PAGE: Parametric Analysis of Gene Set Enrichment , 2005, BMC Bioinform..

[19]  David Botstein,et al.  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..

[20]  May D. Wang,et al.  GoMiner: a resource for biological interpretation of genomic and proteomic data , 2003, Genome Biology.

[21]  John D. Storey.  A direct approach to false discovery rates , 2002 .

[22]  Emden R. Gansner,et al.  An open graph visualization system and its applications to software engineering , 2000, Softw. Pract. Exp..

[23]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.