Biomedical subjects

Kangyu Zhang

Publications and source records attributed to Kangyu Zhang.

4 recordsLinked to original sources

PubMed2006

Gene Aging Nexus: a web database and data mining platform for microarray data on aging.

The recent development of microarray technology provided unprecedented opportunities to understand the genetic basis of aging. So far, many microarray studies have addressed aging-related expression patterns in multiple organisms and under different conditions. The number of relevant studies continues to increase rapidly. However, efficient exploitation of these vast data is frustrated by the lack of an integrated data mining platform or other unifying bioinformatic resource to enable convenient cross-laboratory searches of array signals. To facilitate the integrative analysis of microarray data on aging, we developed a web database and analysis platform 'Gene Aging Nexus' (GAN) that is freely accessible to the research community to query/analyze/visualize cross-platform and cross-species microarray data on aging. By providing the possibility of integrative microarray analysis, GAN should be useful in building the systems-biology understanding of aging. GAN is accessible at http://gan.usc.edu.

Aging↗

PubMed2006

Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.

The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module.

Algorithms↗

PubMed2005

Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites.

Several tests of neutral evolution employ the observed number of segregating sites and properties of the haplotype frequency distribution as summary statistics and use simulations to obtain rejection probabilities. Here we develop a "haplotype configuration test" of neutrality (HCT) based on the full haplotype frequency distribution. To enable exact computation of rejection probabilities for small samples, we derive a recursion under the standard coalescent model for the joint distribution of the haplotype frequencies and the number of segregating sites. For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster.

Chromosome Segregation↗

PubMed2002

Defected expression of E-cadherin in non-small cell lung cancer.

Reduced expression of E-cadherin, a cell-cell adhesion molecule, was frequently observed in several types of human carcinomas, and the protein plays a role as an invasion suppressor in vitro. In an attempt to evaluate the significance of E-cadherin gene in non-small cell lung cancer (NSCLC), we undertook the immunohistochemical and molecule structural analyses of E-cadherin gene in 40 resection specimens of NSCLC and the corresponding paracarcinoma controls. E-cadherin expression was explored by immunohistochemistry with a monoclonal antibody, and the E-cadherin gene was studied by polymerase chain reaction single-strand conformation polymorphism analysis (PCR-SSCP). The analysis represented in this study demonstrated clear reduction in the expression of E-cadherin proteins in the cancer tissues. However, only in one amplicon were aberrant bands detected, which was a single polymorphic site (codon 692; exon 13), and no somatic mutation was found. These results indicated that defected E-cadherin expression might play a role in the development of malignant phenotype in NSCLC, even though the genetic mutation of E-cadherin gene is not involved in the pathogenesis of NSCLC and does not appear to be direct cause for the reduced expression of E-cadherin gene.

Adenocarcinoma↗