The limitations of simple gene set enrichment analysis assuming gene independence

Multiple testing for gene sets from microarray experiments

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Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases

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De-correlating expression in gene-set analysis

(2010) D. Nam   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

(2010) Daniel M Gatti et al.   BMC GENOMICS

Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway

(2010) Zainab Jagani et al.   NATURE MEDICINE

MYC regulation of a “poor-prognosis” metastatic cancer cell state

(2010) Anita Wolfer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene set enrichment analysis made simple

(2010) Rafael A Irizarry et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Gene ranking and biomarker discovery under correlation

(2009) V. Zuber et al.   BIOINFORMATICS

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

(2009) David A. Barbie et al.   NATURE

COFECO: composite function annotation enriched by protein complex data

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A statistical framework for testing functional categories in microarray data

(2008) William T. Barry et al.   Annals of Applied Statistics

FunNet: an integrative tool for exploring transcriptional interactions

(2008) Edi Prifti et al.   BIOINFORMATICS

Modeling Genomic Diversity and Tumor Dependency in Malignant Melanoma

(2008) W. M. Lin et al.   CANCER RESEARCH

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

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

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology

An Integrated Approach for the Analysis of Biological Pathways using Mixed Models

(2008) Lily Wang et al.   PLoS Genetics

An Erythroid Differentiation Signature Predicts Response to Lenalidomide in Myelodysplastic Syndrome

(2008) Benjamin L Ebert et al.   PLOS MEDICINE