Inferring the functional effect of gene expression changes in signaling pathways

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

graphite - a Bioconductor package to convert pathway topology to gene network

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

Along signal paths: an empirical gene set approach exploiting pathway topology

(2012) Paolo Martini et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

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

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

(2010) F. Garcia-Alcalde et al.   BIOINFORMATICS

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

ChiBE: interactive visualization and manipulation of BioPAX pathway models

(2009) Ozgun Babur et al.   BIOINFORMATICS

Wnt/Planar cell polarity signaling: A new paradigm for cancer therapy

(2009) Y. Wang   MOLECULAR CANCER THERAPEUTICS