"BACKGROUND: In this study, differential gene expression analysis using complementary DNA (cDNA) libraries has been improved. Firstly by the introduction of an accurate method of assigning Expressed Sequence Tags (ESTs) to genes and secondly, by using a novel likelihood ratio statistical scoring of differential gene expression between two pools of cDNA libraries. These methods were applied to the latest available cell line and bulk tissue cDNA libraries in a two-step screen to predict novel tumour endothelial markers.

"Epithelial ovarian cancer is the deadliest female reproductive tract malignancy in Western countries. Less than 25% of cases are diagnosed when the cancer is confined, however, pointing to the critical need for early diagnostics for ovarian cancer. Identifying the changes that occur in the glycome of ovarian cancer cells may provide an avenue to develop a new generation of potential biomarkers for early detection of this disease. We performed a glycotranscriptomic analysis of endometrioid ovarian carcinoma using human tissue, as well as a newly developed mouse model that mimics this disease.

"In this new era of cancer genomics, large-scale queries of whole genomic characteristics are now possible not only for research and biological understanding, but also for molecular profiling in the context of patient management and care. Here, we will examine genomic, transcriptomic and proteomic methods of characterizing tumors that may play a role in early diagnosis, classification, prognosis, therapeutic guidance and recurrence surveillance during the entire progression of the disease and treatment cycle.

"Identification of molecular alterations in biological fluids has been proposed as a powerful tool for cancer diagnosis. The purpose of this study was to identify cells that carry chromosomal alterations indicative of malignancy-specifically, gains in the loci 5p15.2 (D5S23, D5S721), 6p11 approximately q11, 7p12 (EGFR), and 8q24.12 approximately q24.13 (MYC)-for the detection of lung cancer using induced sputum. The overall sensitivity of the multicolor fluorescence in situ hybridization (FISH) assay from 52 lung cancer patients was 71% and the specificity was 100% (15 of 15).

"CONTEXT: Gene expression profiling may be useful for prognostic and therapeutic strategies in breast carcinoma. OBJECTIVES: To demonstrate the value in integrating genomic information with clinical and pathological risk factors, to refine prognosis, and to improve therapeutic strategies for early stage breast cancer.

"The androgen receptor (AR) is a transcription factor belonging to the family of nuclear receptors that mediate the action of androgen. AR plays an important role in normal development of the prostate, as well as in the progression of prostate cancer. AR is regulated by several posttranslational modifications, including phosphorylation, acetylation, and ubiquitination.

"OBJECTIVE: Early detection is paramount to reduce the high death rate of ovarian cancer. Unfortunately, current detection tool is not sensitive. New techniques such as deoxyribonucleic acid (DNA) micro-array and proteomics data are difficult to analyze due to high dimensionality, whereas conventional methods such as blood test are neither sensitive nor specific. METHODS: Thus, a functional model of human pattern recognition known as complementary learning fuzzy neural network (CLFNN) is proposed to aid existing diagnosis methods.

"It is a consensus in microarray analysis that identifying potential local patterns, characterized by coherent groups of genes and conditions, may shed light on the discovery of previously undetectable biological cellular processes of genes as well as macroscopic phenotypes of related samples. In order to simultaneously cluster genes and conditions, we have previously developed a fast co-clustering algorithm, Minimum Sum-Squared Residue Co-clustering (MSSRCC), which employs an alternating minimization scheme and generates what we call co-clusters in a checkerboard structure.

"PURPOSE: Alterations of the androgen receptor (AR)-mediated signaling through numerous mechanisms are increasingly recognized in prostate cancer (CaP) progression. We hypothesized that the assessment of well-defined AR transcriptional targets (e.g., PSA/HK3 mRNA) in CaP tissues will provide in vivo readout of AR dysfunctions. Moreover, quantitative expression features of PSA/HK3 mRNA in prostate tumor cells may serve as a prognostic indicator of disease progression.

"PURPOSE: The study aim to identify novel molecular subtypes of ovarian cancer by gene expression profiling with linkage to clinical and pathologic features. EXPERIMENTAL DESIGN: Microarray gene expression profiling was done on 285 serous and endometrioid tumors of the ovary, peritoneum, and fallopian tube. K-means clustering was applied to identify robust molecular subtypes. Statistical analysis identified differentially expressed genes, pathways, and gene ontologies. Laser capture microdissection, pathology review, and immunohistochemistry validated the array-based findings.