FIDEA: a server for the functional interpretation of differential expression analysis

Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis

(2012) Rosa A. Uribe et al.   DEVELOPMENTAL BIOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics

(2012) D. Tabas-Madrid et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

(2012) Décio L. Eizirik et al.   PLoS Genetics

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

(2009) Galina V. Glazko et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH