Deriving transcriptional programs and functional processes from gene expression databases

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Content-based microarray search using differential expression profiles

(2011) Jesse M Engreitz et al.   BMC BIOINFORMATICS

Genome profiling of ERBB2-amplified breast cancers

(2010) Fabrice Sircoulomb et al.   BMC CANCER

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Independent component analysis: Mining microarray data for fundamental human gene expression modules

(2010) Jesse M. Engreitz et al.   JOURNAL OF BIOMEDICAL INFORMATICS

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

A pathway-based classification of human breast cancer

(2010) M. L. Gatza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

(2009) Yao Yu et al.   BMC BIOINFORMATICS

Latent Bone Metastasis in Breast Cancer Tied to Src-Dependent Survival Signals

(2009) Xiang H.-F. Zhang et al.   CANCER CELL

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Nuclear architecture and gene regulation

(2008) Elena Fedorova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

(2008) Y. Zhu et al.   BIOINFORMATICS

An E2F1-Dependent Gene Expression Program that Determines the Balance between Proliferation and Cell Death

(2008) Timothy C. Hallstrom et al.   CANCER CELL

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

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

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

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

(2008) Z. Bar-Joseph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

(2008) Zhandong Liu et al.   GENOME BIOLOGY