PedGenie: meta genetic association testing in mixed family and case-control designs

Background

With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO).

Results

We present the freely available software package GOSim, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. GOSim extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. GOSim hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes.

Conclusion

GOSim is implemented as a package for the statistical computing environment R and is distributed under GPL within the CRAN project.     

MarVis: a tool for clustering and visualization of metabolic biomarkers

Background

Gene set analysis based on Gene Ontology (GO) can be a promising method for the analysis of differential expression patterns. However, current studies that focus on individual GO terms have limited analytical power, because the complex structure of GO introduces strong dependencies among the terms, and some genes that are annotated to a GO term cannot be found by statistically significant enrichment.

Results

We proposed a method for enriching clustered GO terms based on semantic similarity, namely cluster enrichment analysis based on GO (CeaGO), to extend the individual term analysis method. Using an Affymetrix HGU95aV2 chip dataset with simulated gene sets, we illustrated that CeaGO was sensitive enough to detect moderate expression changes. When compared to parent-based individual term analysis methods, the results showed that CeaGO may provide more accurate differentiation of gene expression results. When used with two acute leukemia (ALL and ALL/AML) microarray expression datasets, CeaGO correctly identified specifically enriched GO groups that were overlooked by other individual test methods.

Conclusion

By applying CeaGO to both simulated and real microarray data, we showed that this approach could enhance the interpretation of microarray experiments. CeaGO is currently available at http://chgc.sh.cn/en/software/CeaGO/.     

Arginine increases genotoxicity induced by methyl methanesulfonate in human lymphocytes

Nitric oxide (NO) is a free radical that is produced in cells from l-arginine. NO is involved in the physiological control of different tissues, but it can act as a toxic mediator in the cells. In this study we investigated the effect of l-arginine on the genotoxicity induced by methyl methanesulfonate (MMS) in human lymphocytes. Blood was treated with N^G-nitro-l-arginine methyl ester (l-NAME) as an inhibitor of nitric oxide synthase for finding out the role of NO in this effect. Human whole blood was treated with l-arginine (50, 100 and 250 μM) and/or l-NAME, then it was treated in vitro with MMS after 24 h of culture. The lymphocytes were stimulated by phytohemagglutinin to find out the micronuclei in cytokinesis-blocked binucleated cells. DNA fragmentation of lymphocytes was detected by using a fluorescence microscope after propidium iodide staining. These data showed that arginine increased the frequency of MMS-induced micronuclei in lymphocytes. However, the genotoxicity was decreased by using l-NAME. Arginine and l-NAME have not shown any DNA damage in cultured human lymphocytes. In conclusion, addition of l-arginine to MMS as an alkylating agent caused an increase of DNA damage in human lymphocytes. This enhancement of genotoxicity was reduced by NAME as NO inhibitor. It is thus cleared that an increase of DNA damage by arginine and MMS is related to NO production.     

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Background

Novel tuberculosis (TB) vaccines recently tested in humans have been designed to boost immunity induced by the current vaccine, Mycobacterium bovis Bacille Calmette-Guérin (BCG). Because BCG vaccination is used extensively in infants, this population group is likely to be the first in which efficacy trials of new vaccines will be conducted. However, our understanding of the complexity of immunity to BCG in infants is inadequate, making interpretation of vaccine-induced immune responses difficult.

Methods

To better understand BCG-induced immunity, we performed gene expression profiling in five 10-week old infants routinely vaccinated with BCG at birth. RNA was extracted from 12 hour BCG-stimulated or purified protein derivative of tuberculin (PPD)-stimulated PBMC, isolated from neonatal blood collected 10 weeks after vaccination. RNA was hybridised to the Sentrix^® HumanRef-8 Expression BeadChip (Illumina) to measure expression of >16,000 genes.

Results

We found that ex vivo stimulation of PBMC with PPD and BCG induced largely similar gene expression profiles, except that BCG induced greater macrophage activation. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, including PPAR-γ, involved in activation of the alternative, anti-inflammatory macrophage response was down-regulated following stimulation with both antigens. In contrast, up-regulation of genes associated with the classic, pro-inflammatory macrophage response was noted. Further analysis revealed a decrease in the expression of cell adhesion molecules (CAMs), including integrin alpha M (ITGAM), which is known to be important for entry of mycobacteria into the macrophage. Interestingly, more leukocyte genes were down-regulated than up-regulated.

Conclusion

Our results suggest that a combination of suppressed and up-regulated genes may be key in determining development of protective immunity to TB induced by vaccination with BCG.     

Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis

Background

Exposure to vanadium pentoxide (V₂O₅) is a cause of occupational bronchitis. We evaluated gene expression profiles in cultured human lung fibroblasts exposed to V₂O₅ in vitro in order to identify candidate genes that could play a role in inflammation, fibrosis, and repair during the pathogenesis of V₂O₅-induced bronchitis.

Methods

Normal human lung fibroblasts were exposed to V₂O₅ in a time course experiment. Gene expression was measured at various time points over a 24 hr period using the Affymetrix Human Genome U133A 2.0 Array. Selected genes that were significantly changed in the microarray experiment were validated by RT-PCR.

Results

V₂O₅ altered more than 1,400 genes, of which ~300 were induced while >1,100 genes were suppressed. Gene ontology categories (GO) categories unique to induced genes included inflammatory response and immune response, while GO catogories unique to suppressed genes included ubiquitin cycle and cell cycle. A dozen genes were validated by RT-PCR, including growth factors (HBEGF, VEGF, CTGF), chemokines (IL8, CXCL9, CXCL10), oxidative stress response genes (SOD2, PIPOX, OXR1), and DNA-binding proteins (GAS1, STAT1).

Conclusion

Our study identified a variety of genes that could play pivotal roles in inflammation, fibrosis and repair during V₂O₅-induced bronchitis. The induction of genes that mediate inflammation and immune responses, as well as suppression of genes involved in growth arrest appear to be important to the lung fibrotic reaction to V₂O₅.