John A. Foekens8
John A Foekens6
8John A. Foekens
6John A Foekens
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  • Jack X Yu, Anieta M Sieuwerts, Yi Zhang, John WM Martens, Marcel Smid, Jan GM Klijn +2 others
  • 2007
BACKGROUND Published prognostic gene signatures in breast cancer have few genes in common. Here we provide a rationale for this observation by studying the prognostic power and the underlying biological pathways of different gene signatures. METHODS Gene signatures to predict the development of metastases in estrogen receptor-positive and estrogen(More)
MOTIVATION Retrieval of information on biological processes from large-scale expression data is still a time-consuming task. An automated analysis utilizing all expression information would greatly increase our understanding of the samples under study. RESULTS We describe here a novel method to obtain a functional analysis of complex gene expression data.(More)
MOTIVATION To evaluate microarray data, clustering is widely used to group biological samples or genes. However, problems arise when comparing heterologous databases. As the clustering algorithm searches for similarities between experiments, it will most likely first separate the data sets, masking relationships that exist between samples from different(More)
Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer cell lines to identify miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations.(More)
  • Xiang H.-F. Zhang, Xin Jin, Srinivas Malladi, Yilong Zou, Yong H. Wen, Edi Brogi +3 others
  • 2013
How organ-specific metastatic traits arise in primary tumors remains unknown. Here, we show a role of the breast tumor stroma in selecting cancer cells that are primed for metastasis in bone. Cancer-associated fibroblasts (CAFs) in triple-negative (TN) breast tumors skew heterogeneous cancer cell populations toward a predominance of clones that thrive on(More)
BACKGROUND Clinical outcome of patients with triple-negative breast cancer (TNBC) is highly variable. This study aims to identify and validate a prognostic protein signature for TNBC patients to reduce unnecessary adjuvant systemic therapy. METHODS Frozen primary tumors were collected from 126 lymph node-negative and adjuvant therapy-naive TNBC patients.(More)
BACKGROUND SRS (Sequence Retrieval System) has proven to be a valuable platform for storing, linking, and querying biological databases. Due to the availability of a broad range of different scientific databases in SRS, it has become a useful platform to incorporate and mine microarray data to facilitate the analyses of biological questions and(More)
Increasing knowledge about signal transduction pathways as drivers of cancer growth has elicited the development of "targeted drugs," which inhibit aberrant signaling pathways. They require a companion diagnostic test that identifies the tumor-driving pathway; however, currently available tests like estrogen receptor (ER) protein expression for hormonal(More)
  • Corine M. Beaufort, Jean C. A. Helmijr, Anna M. Piskorz, Marlous Hoogstraat, Kirsten Ruigrok-Ritstier, Nicolle Besselink +9 others
  • 2014
Epithelial ovarian cancer is a highly heterogeneous disease and remains the most lethal gynaecological malignancy in the Western world. Therapeutic approaches need to account for inter-patient and intra-tumoural heterogeneity and detailed characterization of in vitro models representing the different histological and molecular ovarian cancer subtypes is(More)
BACKGROUND Genetic alterations in cellular signaling networks are a hallmark of cancer, however, effective methods to discover them are lacking. A novel form of abnormality called acquired uniparental disomy (aUPD) was recently found to pinpoint the region of mutated genes in various cancers, thereby identifying the region for next-generation sequencing. (More)