CAsubtype: An R Package to Identify Gene Sets Predictive of Cancer Subtypes and Clinical Outcomes

Gene expression analysis identifies global gene dosage sensitivity in cancer

(2015) Rudolf S N Fehrmann et al.   NATURE GENETICS

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

(2015) Razvan Cristescu et al.   NATURE MEDICINE

Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer

(2015) Andrew E Teschendorff et al.   GENOME BIOLOGY

Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients

(2014) T. Z. Tan et al.   EMBO Molecular Medicine

The REST Gene Signature Predicts Drug Sensitivity in Neuroblastoma Cell Lines and Is Significantly Associated with Neuroblastoma Tumor Stage

(2014) Jianfeng Liang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes

(2014) Sharmistha Pal et al.   NUCLEIC ACIDS RESEARCH

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

(2013) N. Rapin et al.   BLOOD

EMT is the dominant program in human colon cancer

(2013) Andre Loboda et al.   BMC Medical Genomics

Prognostic impact of EMT (epithelial-mesenchymal-transition)-related protein expression in endometrial cancer

(2013) Yoshimichi Tanaka et al.   CANCER BIOLOGY & THERAPY

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

(2013) Felipe De Sousa E Melo et al.   NATURE MEDICINE

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

(2013) Anguraj Sadanandam et al.   NATURE MEDICINE

A Prognostic Gene Signature for Metastasis-Free Survival of Triple Negative Breast Cancer Patients

(2013) UnJin Lee et al.   PLoS One

Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value

(2013) Laetitia Marisa et al.   PLOS MEDICINE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Methylation Subtypes and Large-Scale Epigenetic Alterations in Gastric Cancer

(2012) H. Zouridis et al.   Science Translational Medicine

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Making sense of cancer genomic data

(2011) Lynda Chin et al.   GENES & DEVELOPMENT

EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer

(2010) A Singh et al.   ONCOGENE

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY