Sage Uses In Human Genome Mining And Annotation

As previously mentioned, SAGE data is perpetual, and available databases become constantly updated in parallel with our constant improvement in understanding the complete human genome. A recent development of value in helping to better mine the human genome was the report of a modification of the SAGE technique that allows one to obtain longer SAGE tags. This will lead to a better and unique gene identification of the 3' ends of genes and, in turn, facilitates the isolation of novel genes. This...

Unsupervised Learning Clustering

In unsupervised learning techniques, the structure in a data set is elucidated without using any a priori assumptions or knowledge as part of exploratory data analysis. The promise of these methods lies in their ability to provide a molecular grouping or taxonomy of samples or genes. One of the easiest ways to analyze data in this context is by using a clustering algorithm (11-13). Objects of interest, usually genes or samples, are Fig. 2. General methodology for clustering gene expression...

Clinical Manifestations Of Colorectal Cancer

A major goal of global expression analysis is to provide information that supports an enriched system of classification, either alone or in conjunction with clinical and genetic data. To place this effort in perspective, we sketch the clinical behavior of colon cancer and outline the major clinical-pathological classification systems. Adenocarcinoma arises in the epithelial cells of the colon. The tumor consists of a mass of abnormal glands (hence the name, adenocarcinoma) that invades and,...

Experimental Biology Of Prostate Cancer

Several excellent reviews of the molecular biology of prostate cancer are available, and only a few of the more common molecular alterations and their potential significance are highlighted here (4,12). The analysis of chromosomal alterations in cancer has identified many changes reflecting loss or gain of function of particular genes. Consistent allelic loss is expected to reflect the location of putative tumor suppressor genes. Loss of heterozygosity at chromosome arms 8p, 10q, 13q, and 17p...

Results From Expression Profiling Studies Of Lung Carcinomas Reveals Distinct Adenocarcinoma Subclasses

Transciptome Analysis in Lung Tumors Although the SCLC and NSCLC distinction is widely accepted in the context of lung tumor classification, such a classification is based primarily on clinical and pathological attributes of the disease rather than similarity or dissimilarity at the level of biological circuitry. Thus, a basic purpose of transcriptional profiling of lung tumors aims at understanding the molecular view of lung tumors that is relevant from a diagnostic or therapeutic perspective....

General Aspects Of The Pancreas Transcriptome

Before we discuss recent developments in global analyses of gene expression in pancreatic cancer, it would be worthwhile to review what is known about gene expression in pancreatic cancer at the present time. A number of genes expressed in pancreatic ductal adenocarcinomas have been identified over the past 20 yr using a variety of techniques. These genes are summarized in Table 1. Normal pancreatic duct epithelial cells express the cytokeratins 7, 8, 18, and 19 18 . Occasional expression of...

Erbb3

Expression Patterns Related to ER Status Tamoxifen is a frequently prescribed drug for treatment and prevention of breast cancer 7,11,90 . ER tumors may initially respond to tamoxifen, but the development of tamoxifen resistance is an important clinical problem. A number of groups have compared microarray data of breast carcinomas based on ER status. Hilsenbeck et al. 91 compared gene expression arrays of estrogen-stimulated, tamoxifen-sensitive, and resistant MCF-7 cells grown in a nude mouse...

Acta2

Cell adhesion, migration, cytoskeleton, and extracellular matrix Rank Exp met 30 I FHL1 Four and a half LIM domains 1. 47 t HMMR Hyaluronan-mediated motility receptor RHAMM . 61 TPM3 Tropomyosin 3 nonmuscle . 80 t THBS2 Thrombospondin 2. 82 RARRES1 Retinoic acid receptor responder tazarotene-induced 1. 97 CEACAM7 Carcinoembryonic antigen-related cell adhesion Metabolism, biosynthesis, and molecular transport 4 ABCB1 P glycoprotein 1 multiple drug resistance 1. 10 t PGK1 Phosphoglycerate kinase...

W27939

P solute carrier family lo KJAAOS28 phospholipase A2, group X progastricsin pepsinogen C cytokine receptor-like factor I dual specificity phosphatase 4 ornithine decarboxylase I ornithine decarboxylase I TS deleted in oral cancer-related I ribosomal S6 sodium channel, nonvohaee-eated I a DKFZP56400 amp 23 glutathione S-tran Ferase pi glutathione S-transferase pi heps in surfactant, puEmcmary-assoc. prot. B N-acylsphingosine amidohydrolase cytochrome b-5 cvtochromc...

Concluding Remarks

It is clear that the combination of the entire genome sequence, microdissection, and comprehensive expression analysis will have a significant effect on research in cancer biology and oncology. It is also clear that these techniques should be used with discretion, common sense, and healthy skepticism to avoid over interpretation of the large volumes of data, much of which has yet to be validated as reliable. Nonetheless, a carefully controlled experimental design and rigorous data analysis...