Biomedical subjects

Wenxuan Zhong

Publications and source records attributed to Wenxuan Zhong.

4 recordsLinked to original sources

PubMed2006

Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae.

BACKGROUND: Histone acetylation plays important but incompletely understood roles in gene regulation. A comprehensive understanding of the regulatory role of histone acetylation is difficult because many different histone acetylation patterns exist and their effects are confounded by other factors, such as the transcription factor binding sequence motif information and nucleosome occupancy. RESULTS: We analyzed recent genomewide histone acetylation data using a few complementary statistical models and tested the validity of a cumulative model in approximating the global regulatory effect of histone acetylation. Confounding effects due to transcription factor binding sequence information were estimated by using two independent motif-based algorithms followed by a variable selection method. We found that the sequence information has a significant role in regulating transcription, and we also found a clear additional histone acetylation effect. Our model fits well with observed genome-wide data. Strikingly, including more complicated combinatorial effects does not improve the model's performance. Through a statistical analysis of conditional independence, we found that H4 acetylation may not have significant direct impact on global gene expression. CONCLUSION: Decoding the combinatorial complexity of histone modification requires not only new data but also new methods to analyze the data. Our statistical analysis confirms that histone acetylation has a significant effect on gene transcription rates in addition to that attributable to upstream sequence motifs. Our analysis also suggests that a cumulative effect model for global histone acetylation is justified, although a more complex histone code may be important at specific gene loci. We also found that the regulatory roles among different histone acetylation sites have important differences.

Acetylation↗

PubMed2006

A data-driven clustering method for time course gene expression data.

Gene expression over time is, biologically, a continuous process and can thus be represented by a continuous function, i.e. a curve. Individual genes often share similar expression patterns (functional forms). However, the shape of each function, the number of such functions, and the genes that share similar functional forms are typically unknown. Here we introduce an approach that allows direct discovery of related patterns of gene expression and their underlying functions (curves) from data without a priori specification of either cluster number or functional form. Smoothing spline clustering (SSC) models natural properties of gene expression over time, taking into account natural differences in gene expression within a cluster of similarly expressed genes, the effects of experimental measurement error, and missing data. Furthermore, SSC provides a visual summary of each cluster's gene expression function and goodness-of-fit by way of a 'mean curve' construct and its associated confidence bands. We apply this method to gene expression data over the life-cycle of Drosophila melanogaster and Caenorhabditis elegans to discover 17 and 16 unique patterns of gene expression in each species, respectively. New and previously described expression patterns in both species are discovered, the majority of which are biologically meaningful and exhibit statistically significant gene function enrichment. Software and source code implementing the algorithm, SSClust, is freely available (http://genemerge.bioteam.net/SSClust.html).

Algorithms↗

PubMed2005

RSIR: regularized sliced inverse regression for motif discovery.

MOTIVATION: Identification of transcription factor binding motifs (TFBMs) is a crucial first step towards the understanding of regulatory circuitries controlling the expression of genes. In this paper, we propose a novel procedure called regularized sliced inverse regression (RSIR) for identifying TFBMs. RSIR follows a recent trend to combine information contained in both gene expression measurements and genes' promoter sequences. Compared with existing methods, RSIR is efficient in computation, very stable for data with high dimensionality and high collinearity, and improves motif detection sensitivities and specificities by avoiding inappropriate model specification. RESULTS: We compare RSIR with SIR and stepwise regression based on simulated data and find that RSIR has a lower false positive rate. We also demonstrate an excellent performance of RSIR by applying it to the yeast amino acid starvation data and cell cycle data. AVAILABILITY: Matlab programs are available upon request from the authors.

Algorithms↗

PubMed2005

Detection of synovial macrophages in the joint capsule of dogs with naturally occurring rupture of the cranial cruciate ligament.

OBJECTIVE: To test the hypotheses that the densities of macrophages in the synovial membranes and capsules of stifle joints in dogs with ruptured cranial cruciate ligaments are greater than those of normal joints and that those densities in affected joints are positively correlated with the chronicity and severity of the disease. ANIMALS: 17 dogs with naturally occurring rupture of the cranial cruciate ligament and 5 healthy control dogs. PROCEDURE: All dogs underwent orthopedic and radiographic evaluations. In affected dogs, duration of clinical signs was used as an indicator of disease chronicity and the severity of osteoarthritis in the stifle joint was determined radiographically. Joint capsule specimens were evaluated histologically; macrophages, interleukin-6, and tumor necrosis factor-alpha were identified by use of immunocytochemical techniques. RESULTS: Compared with unaffected joints, macrophage density was increased in all affected joints. Duration of disease was significantly associated with radiographic severity of osteoarthritis and synovial macrophage density. Synovial macrophage density was significantly associated with severity of osteoarthritis and with the presence of interleukin-6 and tumor necrosis factor-a. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that synovial macrophages may be involved in the development of pathologic changes (including osteophyte formation) in the stifle joints of dogs with osteoarthritis secondary to rupture of the cranial cruciate ligament. Determination of the importance of synovial macrophages in the development of changes in osteoarthritic joints may result in new treatment strategies that involve elimination of the deleterious effects of those cells.

Animals↗