The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.
Gene Ontology ; Microarray Analysis ; Protein Interaction Maps

Antigens ; analysis ; Microarray Analysis ; methods ; Quantum Dots ; Semiconductors

OBJECTIVETo establish a novel suspension microarray technology for the detection of three kinds of veterinary drug residues: chloramphenicol, clenbuterol and 17-beta-estradiol (CAP, CL and E2).

METHODSThe three conjugates that veterinary drug coupled with bovine serum albumin (BSA) were synthesized and identified by ultraviolet (UV) spectrophotometry and mass spectrum. The veterinary drug conjugates were immobilized on the polystyrene fluorescent microspheres/beads. There were competitive reactions between the veterinary drugs in the aqueous phase and that on the beads for combination with their specific biotinylated monoclonal antibodies. The optimum amount of the veterinary drug conjugates and the antibodies were optimized and selected. The detective standard curves were plotted. The specificity and the unknown samples were also determined by grouping according to different concentrations of the interferes and the samples. Meantime, the different microstructures of the surfaces of the beads were also observed by scanning electron microscope.

RESULTSCouplings were completed between small molecular veterinary drugs and BSA. The amounts of the three conjugates and the antibodies were optimized. The detective standard curves of the suspension array and their corresponding coefficients of determination (R2) were good (R2 > 0.99). The detection ranges of the three veterinary drugs were (40.00 - 6.25) x 10(5) ng/L, (50.00-7.81) x 10(5) ng/L and 1.00 x 10(3) - 7.29 x 10(5) ng/L respectively. Simultaneously, the specific detection of the suspension microarray was excellent and did not indicate significant cross-reactions. Errors between the found and the real are in the range of 8.09% - 17.03%. It can be considered that the relative standard deviations were relatively small. Successful couplings were also directly confirmed by the observation for microstructures of the surfaces of the beads by scanning of electron microscope and laid good foundation for the following responses.

CONCLUSIONThe high-throughput suspension microarray should provide a novel method for multi-analysis of the veterinary drugs and have a wide applicative prospects with simple operation, sensitive, rapid and low cost.

Chloramphenicol ; analysis ; Clenbuterol ; analysis ; Drug Residues ; analysis ; Estradiol ; analysis ; Microarray Analysis ; methods ; Veterinary Drugs ; analysis

Biochip reader is an important instrument for taking pictures of biochip. The accuracy of the instrument influences diagnosis of doctors. So it is important to reduce the nonuniformity of images and the error between the biochip readers. This paper describes the development of new standard plane light source, which can reduce the work load of calibration, improve the accuracy and speed of calibration, made the biochip readers more reliably.
Equipment Design ; Lab-On-A-Chip Devices ; Light ; Microarray Analysis

Exercise capacity is a valuable trait in horses, and it has been used as a horse selection criterion. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully described. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively. The expressions of 6 miRNAs, including 4 known and 2 novel miRNAs, were altered by exercise. The predicted target genes of the differentially expressed miRNAs identified by NGS were matched to the exercise-induced mRNAs determined by microarray analysis. Five genes (LOC100050849, LOC100054517, KHDRBS3, LOC100053996, and LOC100062720) from the microarray analysis were matched to the predicted target genes of the 6 miRNAs. The subset of mRNAs and miRNAs affected by exercise in peripheral blood leukocytes may be useful in elucidating the molecular mechanisms of exercise-associated physiology in horses.
Homeostasis ; Horses ; Leukocytes ; Microarray Analysis ; MicroRNAs ; Physiology ; RNA ; RNA, Messenger

Glycosylation is one of the common post-translational modifications of proteins to regulate the ability of tumor invasion, metastasis and tumor heterogeneity by interacting with glycan-binding proteins such as lectins and antibodies. Glycan microarray can be constructed by chemical synthesis, chemical-enzyme synthesis or natural glycan releasing. Glycan microarray is an essential analytical tool to discover the interaction between glycan and its binding proteins. Here we summarize the standard techniques to construct glycan microarray for the application in cancer vaccine, monoclonal antibody and diagnostic markers.
Antibodies, Monoclonal ; Glycosylation ; Lectins/metabolism* ; Microarray Analysis ; Neoplasms ; Polysaccharides

Humans ; Microarray Analysis ; Multiple Myeloma/genetics* ; RNA, Long Noncoding

OBJECTIVE: To examine the mechanism for the inhibited differentiation of osteoclasts in rheumatoid arthritis synovial CD14+ osteoclast precursors, the different expressions of the osteoclastogenesis-related genes in rheumatoid arthritis (RA) synovial fluid CD14+ osteoclast precursors were compared with those of normal peripheral blood (PB) CD14+ osteoclast precursors. METHODS: The expression of osteoclastogenesis-related genes were examined using a gene expression oligonucleotide microarray. To validate the results of the microarray analysis, the mRNA expressions of osteoclastogenesis-related genes were measured by real-time PCR. RESULTS: Comparative analysis of the mRNA profiles showed significantly different expression of osteoclastogenesis- related genes, such as MafB, Id3 and LILRB4, in the RA synovial CD14+ osteoclast precursors, compared to that of normal PB CD14+ osteoclast precursors. CONCLUSION: The expression of the osteoclastogenesis-related genes in RA synovial CD14+ osteoclast precursors is different from that of the normal PB CD14+ osteoclast precursors. These results suggest that the different expression of osteoclastogenesis-related genes might be involved in the altered osteoclastogenesis in RA synovial osteoclast precursors.
Arthritis, Rheumatoid ; Genes, vif ; Macrophages ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Osteoclasts ; RNA, Messenger ; Synovial Fluid

The establishment of DNA microarray technology has enabled high-throughput analysis and molecular profiling of various types of cancers. By using the gene expression data from microarray analysis we are able to investigate diagnostic applications at the molecular level. The most important step in the application of microarray technology to cancer diagnostics is the selection of specific markers from gene expression profiles. In order to select markers of immortalization and transformation we used c-myc and H-ras(V12) oncogene-transfected NIH3T3 cells as our model system. We have identified 8751 differentially expressed genes in the immortalization/transformation model by multivariate permutation F-test (95% confidence, FDR <0.01). Using the support vector machine algorithm, we selected 13 discriminative genes which could be used to predict immortalization and transformation with perfect accuracy. We assayed H-ras(V12)-transfected "transformed" cells to validate our immortalization/transformation classification system. The selected molecular markers generated valuable additional information for tumor diagnosis, prognosis and therapy development.
Classification ; Diagnosis ; Gene Expression ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Prognosis ; Transcriptome ; Support Vector Machine

Human Genome Project (HGP) could unveil the secrets of human being by a long script of genetic codes, which enabled us to get access to mine the cause of diseases more efficiently. Two wheels for HGP, bioinformatics and high throughput technology are essential techniques for the genomic medicine. While microarray platforms are still evolving, we can screen more than 500,000 genotypes at once. Even we can sequence the whole genome of an organism within a day. Because the future medicne will focus on the genetic susceptibility of individuals, we need to find genetic variations of each person by efficient genotyping methods.
Sequence Analysis, DNA ; Microarray Analysis ; Korea ; Humans ; *Human Genome Project ; Genotype ; Genetic Predisposition to Disease ; *Cohort Studies