GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms

Background  

An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions, cellular components, signaling pathways, physiologic processes and diseases.     

Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity

Background

Communalities between large sets of genes obtained from high-throughput experiments are often identified by searching for enrichments of genes with the same Gene Ontology (GO) annotations. The GO analysis tools used for these enrichment analyses assume that GO terms are independent and the semantic distances between all parent–child terms are identical, which is not true in a biological sense. In addition these tools output lists of often redundant or too specific GO terms, which are difficult to interpret in the context of the biological question investigated by the user. Therefore, there is a demand for a robust and reliable method for gene categorization and enrichment analysis.

Results

We have developed Categorizer, a tool that classifies genes into user-defined groups (categories) and calculates p-values for the enrichment of the categories. Categorizer identifies the biologically best-fit category for each gene by taking advantage of a specialized semantic similarity measure for GO terms. We demonstrate that Categorizer provides improved categorization and enrichment results of genetic modifiers of Huntington’s disease compared to a classical GO Slim-based approach or categorizations using other semantic similarity measures.

Conclusion

Categorizer enables more accurate categorizations of genes than currently available methods. This new tool will help experimental and computational biologists analyzing genomic and proteomic data according to their specific needs in a more reliable manner.     

Identifying subset of genes that have influential impacts on cancer progression: a new approach to analyze cancer microarray data

Cancer is a complex genetic disease, resulting from defects of multiple genes. Development of microarray techniques makes it possible to survey the whole genome and detect genes that have influential impacts on the progression of cancer. Statistical analysis of cancer microarray data is challenging because of the high dimensionality and cluster nature of gene expressions. Here, clusters are composed of genes with coordinated pathological functions and/or correlated expressions. In this article, we consider cancer studies where censored survival endpoint is measured along with microarray gene expressions. We propose a hybrid clustering approach, which uses both pathological pathway information retrieved from KEGG and statistical correlations of gene expressions, to construct gene clusters. Cancer survival time is modeled as a linear function of gene expressions. We adopt the clustering threshold gradient directed regularization (CTGDR) method for simultaneous gene cluster selection, within-cluster gene selection, and predictive model building. Analysis of two lymphoma studies shows that the proposed approach - which is composed of the hybrid gene clustering, linear regression model for survival, and clustering regularized estimation with CTGDR - can effectively identify gene clusters and genes within selected clusters that have satisfactory predictive power for censored cancer survival outcomes.     

Atomic force microscopy: a tool to analyze the structural organization of pathogenic protozoa

The fine structure of parasitic protozoa has been the subject of intense investigation with the use of electron microscopy. The recent development of atomic force microscopy (AFM) and all of the techniques associated with AFM has created new ways to further analyze the structure of cells. In this review, the various, presently-available modalities of AFM are discussed, as well as the results obtained in analysis of: (i) the structure of intact and detergent-extracted protozoa; (ii) the surface of infected cells; (iii) the structure of parasite macromolecules; (iv) the measurement of surface potential; and (v) force spectroscopy, the measurement of elasticity and ligand-receptor interactions.     

PGMapper: a web-based tool linking phenotype to genes

SUMMARY: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species. AVAILABILITY: Available online at http://www.genediscovery.org/pgmapper/index.jsp.     

RECA immunological assay as a tool to analyze the SOS response

The content of RECA protein, one of the SOS genes product, was determined in a bacterial extract by a two site-radioimmunometric assay. The variation of the RECA concentration after induction by physical or chemical treatments was used as a probe to analyze the SOS response. Relationships between either the number or the nature of DNA lesions and the level of the relative amplification of RECA have been established. The modulation of the recA gene expression is discussed.     

Vivipary as a tool to analyze late embryogenic events in maize

In maize vivipary, the precocious germination of the seed while still attached to the ear, is the diagnostic phenotype of mutants, which are impaired in the biosynthesis or response to abscisic acid (ABA). Of the 15 genes so far described, 12 control specific steps in ABA biosynthesis, two mediate hormone response and one still has an undefined role. We have analyzed a collection of 25 independent vp isolates with the aim of determining the degree of mutational saturation that has so far been reached. Of the 25 viviparous mutants complementation tested, 22 correspond to known loci: six are allelic to vp1, another six to vp5, one to vp7, two to vp9, six to vp10 and one to w3. The remaining three represent genes not previously identified. All mutants so far tested except rea show a decrease in ABA content. As to the only two mutants (vp1 and rea) whose endogenous ABA content is not impaired, the reduction in sensitivity of the double mutant compared to the single ones suggests that the two genes control separate pathways in the ABA signal transduction. Some of the mutants in this collection have a characteristic incomplete germination that allows the embryo of the mature dry seed to resume germination. By exploiting this feature it is possible to infer, through a germination test, whether the mutant has been impaired in the acquisition of desiccation tolerance. This information provides the starting point for the dissection of the genetic basis of desiccation tolerance.     

Synthesis of affinity-label chelates: a novel synthetic method of coupling ethylenediaminetetraacetic acid to amine functional groups

An affinity-label chelate for the enzyme trypsin was synthesized by a novel synthetic technique which takes advantage of the presence of a dangling carboxylate arm in the [Co(EDTA)Cl]2- complex anion. The dangling carboxylate group was coupled to the amino group of p-aminobenzamidine, an effective inhibitor of trypsin activity, via the carbodiimmide reaction to produce a trypsin affinity label at one end and a strong EDTA-like chelating agent at the other, coupled through an amide bond. The cobalt ion can be removed if desired by reduction with Fe2+ + ascorbate, and alternate metal ions inserted in its place. The reaction is general, and affinity labels which contain amino groups can be easily coupled via this procedure, allowing the introduction of a paramagnetic or fluorescent probe into a protein or nucleotide system. The same method has been used to prepare a highly effective chelating gel which is capable of removing calcium and lanthanide ions from the binding protein parvalbumin.     

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

We present a simple but powerful procedure to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure has been implemented as a web application, FatiGO, allowing for easy and interactive querying. FatiGO, which takes the multiple-testing nature of statistical contrast into account, currently includes GO associations for diverse organisms (human, mouse, fly, worm and yeast) and the TrEMBL/Swissprot GOAnnotations@EBI correspondences from the European Bioinformatics Institute.     

Programmed delivery of novel functional groups to the alpha class glutathione transferases

Here we describe a new route to site- and class-specific protein modification that will allow us to create novel functional proteins with artificial chemical groups. Glutathione transferases from the alpha but not the mu, pi, omega, or theta classes can be rapidly and site-specifically acylated with thioesters of glutathione (GS-thioesters) that are similar to compounds that have been demonstrated to occur in vivo. The human isoforms A1-1, A2-2, A3-3, and A4-4 from the alpha class all react with the reagent at a conserved tyrosine residue (Y9) that is crucial in catalysis of detoxication reactions. The yield of modified protein is virtually quantitative in less than 30 min under optimized conditions. The acylated product is stable for more than 24 h at pH 7 and 25 degrees C. The modification is reversible in the presence of excess glutathione, but the labeled protein can be protected by adding S-methylglutathione. The stability of the ester with respect to added glutathione depends on the acyl moiety. The reaction can also take place in Escherichia coli lysates doped with alpha class glutathione transferases. A control substance that lacks the peptidyl backbone required for binding to the glutathione transferases acylates surface-exposed lysines. There is some acyl group specificity since one out of the three different GS-thioesters that we tried was not able to acylate Y9.