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Articles by W Song
Total Records ( 6 ) for W Song
  X. Q Xia , M McClelland , S Porwollik , W Song , X Cong and Y. Wang
 

Motivation: Cross-platform microarray analysis is an increasingly important research tool, but researchers still lack open source tools for storing, integrating and analyzing large amounts of microarray data obtained from different array platforms.

Results: An open source integrated microarray database and analysis suite, WebArrayDB (http://www.webarraydb.org), has been developed that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion, and allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

  Y Lu , Y Zhang , N Wang , Z Pan , X Gao , F Zhang , H Shan , X Luo , Y Bai , L Sun , W Song , C Xu , Z Wang and B. Yang
  Background—

A characteristic of both clinical and experimental atrial fibrillation (AF) is atrial electric remodeling associated with profound reduction of L-type Ca2+ current and shortening of the action potential duration. The possibility that microRNAs (miRNAs) may be involved in this process has not been tested. Accordingly, we assessed the potential role of miRNAs in regulating experimental AF.

Methods and Results—

The miRNA transcriptome was analyzed by microarray and verified by real-time reverse-transcription polymerase chain reaction with left atrial samples from dogs with AF established by right atrial tachypacing for 8 weeks and from human atrial samples from AF patients with rheumatic heart disease. miR-223, miR-328, and miR-664 were found to be upregulated by >2 fold, whereas miR-101, miR-320, and miR-499 were downregulated by at least 50%. In particular, miR-328 level was elevated by 3.9-fold in AF dogs and 3.5-fold in AF patients relative to non-AF subjects. Computational prediction identified CACNA1C and CACNB1, which encode cardiac L-type Ca2+ channel 1c- and β1 subunits, respectively, as potential targets for miR-328. Forced expression of miR-328 through adenovirus infection in canine atrium and transgenic approach in mice recapitulated the phenotypes of AF, exemplified by enhanced AF vulnerability, diminished L-type Ca2+ current, and shortened atrial action potential duration. Normalization of miR-328 level with antagomiR reversed the conditions, and genetic knockdown of endogenous miR-328 dampened AF vulnerability. CACNA1C and CACNB1 as the cognate target genes for miR-328 were confirmed by Western blot and luciferase activity assay showing the reciprocal relationship between the levels of miR-328 and L-type Ca2+ channel protein subunits.

Conclusions—

miR-328 contributes to the adverse atrial electric remodeling in AF through targeting L-type Ca2+ channel genes. The study therefore uncovered a novel molecular mechanism for AF and indicated miR-328 as a potential therapeutic target for AF.

  K Tao , N Qian , Y Tang , Z Ti , W Song , D Cao and K. Dou
  Objective

A disintegrin and metalloprotease-9 has been involved in the carcinogenesis of various solid tumors. However, its role in hepatocellular carcinoma remains unknown. The aim of this study was to investigate the clinicopathological and prognostic relevance of a disintegrin and metalloprotease-9 by immunohistochemistry.

Methods

The expression profile of a disintegrin and metalloprotease-9 in association with the clinicopathological factors was determined by immunohistochemical analysis in hepatocellular carcinoma patients, and its potential prognostic value was investigated by comparing the survival rate between a disintegrin and metalloprotease-9-positive and a disintegrin and metalloprotease-9-negative patients.

Results

Hepatocellular carcinoma tissues with positive a disintegrin and metalloprotease-9 expression were larger and less differentiated than those with negative expression (P = 0.02 and 0.008, respectively). Portal venous invasion, hepatic venous invasion, bile duct invasion and intrahepatic metastasis were detected significantly more frequently in a disintegrin and metalloprotease-9-positive group (P = 0.009, 0.01, 0.03 and 0.02, respectively). In addition, high -fetoprotein levels were significantly associated with the expression of a disintegrin and metalloprotease-9 in hepatocellular carcinoma (P = 0.01). Moreover, a disintegrin and metalloprotease-9-positive group had significantly poorer outcomes than a disintegrin and metalloprotease-9-negative group (P = 0.01) and was an independent prognostic factor for overall survival.

Conclusions

A disintegrin and metalloprotease-9 is over-expressed in hepatocellular carcinoma tissues, consistent with findings in other tumor entities, and is an independent prognostic marker of overall survival following hepatectomy. Further studies are needed to investigate the precise function of a disintegrin and metalloprotease-9 in the progression of hepatocellular carcinoma.

  X Wang , W Song , Z Yang , Y Wang , Z Tang and C. Xu
 

The endosperm in plants is a major source of human nutrition and industrial raw material. The genetic study of endosperm poses a great challenge due to its complex genetic composition and unique physical and developmental properties. In this note, we shall revisit 2 classic mating designs—North Carolina Design III (NCIII) and triple test cross (TTC)—and demonstrate their efficiency in detecting quantitative trait loci underlying endosperm traits.

 
 
 
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