New network topology approaches reveal differential correlation patterns in breast cancer

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

(2013) David Amar et al.   PLoS Computational Biology

Pathway Correlation Profile of Gene-Gene Co-Expression for Identifying Pathway Perturbation

(2012) Allison N. Tegge et al.   PLoS One

Differential C3NET reveals disease networks of direct physical interactions

(2011) Gökmen Altay et al.   BMC BIOINFORMATICS

Androgen receptor expression in primary breast cancer and its predictive and prognostic value in patients treated with neoadjuvant chemotherapy

(2011) Sibylle Loibl et al.   BREAST CANCER RESEARCH AND TREATMENT

Quantitative Determination of Estrogen Receptor, Progesterone Receptor, and HER2 mRNA in Formalin-fixed Paraffin-embedded Tissue—A New Option for Predictive Biomarker Assessment in Breast Cancer

(2011) Berit Maria Müller et al.   DIAGNOSTIC MOLECULAR PATHOLOGY

Genome-wide Gene Expression Profiling of Formalin-fixed Paraffin-Embedded Breast Cancer Core Biopsies Using Microarrays

(2011) Jan Budczies et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

(2010) Bruno M Tesson et al.   BMC BIOINFORMATICS

A semi-parametric Bayesian model for unsupervised differential co-expression analysis

(2010) Johannes M Freudenberg et al.   BMC BIOINFORMATICS

Use of ER/PR/HER2 subtypes in conjunction with the 2007 St Gallen Consensus Statement for early breast cancer

(2010) Katrina Bauer et al.   BMC CANCER

Increased entropy of signal transduction in the cancer metastasis phenotype

(2010) Andrew E Teschendorff et al.   BMC Systems Biology

FOXC1 Is a Potential Prognostic Biomarker with Functional Significance in Basal-like Breast Cancer

(2010) P. S. Ray et al.   CANCER RESEARCH

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Statistical methods for gene set co-expression analysis

(2009) YounJeong Choi et al.   BIOINFORMATICS

An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients

(2009) Balazs Györffy et al.   BREAST CANCER RESEARCH AND TREATMENT

Molecular characterization of apocrine carcinoma of the breast: Validation of an apocrine protein signature in a well-defined cohort

(2009) Julio E. Celis et al.   Molecular Oncology

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules

(2009) Lucinda K. Southworth et al.   PLoS Genetics

Differential dependency network analysis to identify condition-specific topological changes in biological networks

(2008) Bai Zhang et al.   BIOINFORMATICS

15-Prostaglandin Dehydrogenase Expression Alone or in Combination with ACSM1 Defines a Subgroup of the Apocrine Molecular Subtype of Breast Carcinoma

(2008) Julio E. Celis et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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