Biomedical subjects

Wen-Yu Chung

Publications and source records attributed to Wen-Yu Chung.

3 recordsLinked to original sources

PubMed2006

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network.

BACKGROUND: While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most duplicate genes preserve (or subdivide) the functions of the parental gene or acquire new functions. One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes. RESULTS: Here we build a human gene coexpression network using human tissue-specific microarray data and investigate the divergence of duplicate genes in it. The topology of this network is scale-free. Interestingly, our analysis indicates that duplicate genes rapidly lose shared coexpressed partners: after approximately 50 million years since duplication, the two duplicate genes in a pair have only slightly higher number of shared partners as compared with two random singletons. We also show that duplicate gene pairs quickly acquire new coexpressed partners: the average number of partners for a duplicate gene pair is significantly greater than that for a singleton (the latter number can be used as a proxy of the number of partners for a parental singleton gene before duplication). The divergence in gene expression between two duplicates in a pair occurs asymmetrically: one gene usually has more partners than the other one. The network is resilient to both random and degree-based in silico removal of either singletons or duplicate genes. In contrast, the network is especially vulnerable to the removal of highly connected genes when duplicate genes and singletons are considered together. CONCLUSION: Duplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons.

Chromosome Mapping↗

PubMed2004

Individuals' leukocyte DNA double-strand break repair as an indicator of radiosurgery responses for cerebral arteriovenous malformations.

To evaluate the feasibility of using radiosensitivity of peripheral leukocytes as a predictor of clinical therapeutic responses to radiosurgery in individuals with cerebral arteriovenous malformation (AVM), we enrolled 18 patients years after they had received Gamma Knife radiosurgery for their cerebral AVM. The AVMs were shown with different degrees of regression in size in posttherapeutic periods. The peripheral leukocytes of these patients were collected at the last neuroimaging follow-ups. The leukocytes, before and 1 and 2 h after 8 Gy external gamma-irradiation, were evaluated for the amounts of DNA double-strand breaks (DSB) in 50 randomly selected individual nuclei by the neutral single cell gel electrophoresis, or so-called comet analysis. After being adjusted for gender and age at radiosurgery, the individuals with less posttherapeutic regression in AMV sizes or relatively poor or inadequate responses to radiosurgery were shown to have significantly higher DSB repair capacity on their leukocytes by comet analysis. These results suggested that in vitro radiosensitivity of peripheral leukocytes may provide valuable information for predicting therapeutic response or for adjusting irradiation doses in AVM radiosurgery.

Adolescent↗

PubMed2003

ETOPE: Evolutionary test of predicted exons.

Since a large number of computationally predicted exons are not supported by existing sequence (e.g. ESTs) or experimental (e.g. expression analysis) data they need to be validated by other methods. ETOPE is designed to test computational predictions by using signals that have not been included in any current computational prediction method. The test is based on the ratio of non-synonymous to synonymous substitution rates between sequences from different genomes. It has been previously shown, by empirical data and computer simulation, to be a powerful criterion for identifying protein-coding regions. The ETOPE is available at http://nekrut.uchicago.edu/etope/.

Amino Acid Substitution↗