ArrayVigil: a methodology for statistical comparison of gene signatures using segregated-one-tailed (SOT) Wilcoxon's signed-rank test

Due to versatile diagnostic and prognostic fidelity molecular signatures or fingerprints are anticipated as the most powerful tools for cancer management in the near future. Notwithstanding the experimental advancements in microarray technology, methods for analyzing either whole arrays or gene signatures have not been firmly established. Recently, an algorithm, ArraySolver has been reported by Khan for two-group comparison of microarray gene expression data using two-tailed Wilcoxon signed-rank test. Most of the molecular signatures are composed of two sets of genes (hybrid signatures) wherein up-regulation of one set and down-regulation of the other set collectively define the purpose of a gene signature. Since the direction of a selected gene's expression (positive or negative) with respect to a particular disease condition is known, application of one-tailed statistics could be a more relevant choice. A novel method, ArrayVigil, is described for comparing hybrid signatures using segregated-one-tailed (SOT) Wilcoxon signed-rank test and the results compared with integrated-two-tailed (ITT) procedures (SPSS and ArraySolver). ArrayVigil resulted in lower P values than those obtained from ITT statistics while comparing real data from four signatures.     

Lack of evidence for segregation of a single dominant major gene as the cause of the difference in egg weight between two highly inbred lines of chickens

Data on egg weight from experimental crosses with two inbred lines of chickens suggested evidence for segregation of a single dominant major gene. Because the data could not be transformed to satisfy normality and homoscedasticity conditions, the non-parametric test of Elston and the graphical approach used by Stolk et al. were applied. Due to a bad fit of the backcross B2 (P₂×F1) and the F2 groups, both methods reject the hypothesis of a dominant major gene as the the only cause of the differences in egg weight between the six genetic groups involved.     

On the power for linkage detection using a test based on scan statistics

We analyze some aspects of scan statistics, which have been proposed to help for the detection of weak signals in genetic linkage analysis. We derive approximate expressions for the power of a test based on moving averages of the identity by descent allele sharing proportions for pairs of relatives at several contiguous markers. We confirm these approximate formulae by simulation. The results show that when there is a single trait-locus on a chromosome, the test based on the scan statistic is slightly less powerful than that based on the customary allele sharing statistic. On the other hand, if two genes having a moderate effect on a trait lie close to each other on the same chromosome, scan statistics improve power to detect linkage.     

Application of Gibbs sampling for inference in a mixed major gene-polygenic inheritance model in animal populations

The application of Gibbs sampling is considered for inference in a mixed inheritance model in animal populations. Implementation of the Gibbs sampler on scalar components, as used for human populations, appeared not to be efficient, and an approach with blockwise sampling of genotypes was proposed for use in animal populations. The blockwise sampling of genotypes was proposed for use in animal populations. The blockwise sampling by which genotypes of a sire and its final progeny were sampled jointly was effective in improving mixing, although further improvements could be looked for. Posterior densities of parameters were visualised from Gibbs samples; from the former highly marginalised Bayesian point and interval estimates can be obtained.     

Integration of microbial ecology and statistics: a test to compare gene libraries

Libraries of 16S rRNA genes provide insight into the membership of microbial communities. Statistical methods help to determine whether differences in library composition are artifacts of sampling or are due to underlying differences in the communities from which they are derived. To contribute to a growing statistical framework for comparing 16S rRNA libraries, we present a computer program, integral -LIBSHUFF, which calculates the integral form of the Cramér-von Mises statistic. This implementation builds upon the LIBSHUFF program, which uses an approximation of the statistic and makes a number of modifications that improve precision and accuracy. Once integral -LIBSHUFF calculates the P values, when pairwise comparisons are tested at the 0.05 level, the probability of falsely identifying a significant P value is 0.098 for a study with two libraries, 0.265 for three libraries, and 0.460 for four libraries. The potential negative effects of making the multiple pairwise comparisons necessitate correcting for the increased likelihood that differences between treatments are due to chance and do not reflect biological differences. Using integral -LIBSHUFF, we found that previously published 16S rRNA gene libraries constructed from Scottish and Wisconsin soils contained different bacterial lineages. We also analyzed the published libraries constructed for the zebrafish gut microflora and found statistically significant changes in the community during development of the host. These analyses illustrate the power of integral -LIBSHUFF to detect differences between communities, providing the basis for ecological inference about the association of soil productivity or host gene expression and microbial community composition.     

Resistance to potato leaf roll virus multiplication in potato is under major gene control

The concentration of potato leaf roll virus (PLRV), as measured by a quantitative enzyme-linked immunosorbent assay, in the foliage of potato plants (Solanum tuberosum) of cv Maris Piper with secondary infection was 2900 ng/g leaf, whereas in clones G7445(1) and G7032(5) it was 180 ng/g leaf and 120 ng/g leaf, respectively. To examine the genetic control of resistance to PLRV multiplication, reciprocal crosses were made between the susceptible cultivar Maris Piper and the two resistant clones, and the three parents were selfed. Seedling progenies of these families were grown to generate tubers of individual genotypes (clones). Clonally propagated plants were graft-inoculated, and their daughter tubers were collected and used to grow plants with secondary infection in which PLRV concentration was estimated. The expression of resistance to PLRV multiplication had a bimodal distribution in progenies from crosses between Maris Piper and either resistant clone, and also in progeny from selfing the resistant parents, with genotypes segregating into high and low virus titre groups. Only the progeny obtained from selfing Maris Piper did not segregate, all genotypes being susceptible to PLRV multiplication. The pattern of segregation obtained from these progenies fits more closely with the genetical hypothesis that resistance to PLRV multiplication is controlled by two unlinked dominant complementary genes, both of which are required for resistance, than with the simpler hypothesis that resistance is conferred by a single dominant gene, as published previously.     

Statistical techniques for detection of major genes in animal breeding data

Summary Statistical techniques for detection of major loci and for making inferences about major locus parameters such as genotypic frequencies, effects and gene action from field-collected data are presented. In field data, major genotypic effects are likely to be masked by a large number of environmental differences in addition to additive and nonadditive polygenic effects. A graphical technique and a procedure for discriminating among genetic hypotheses based on a mixed model accounting for all these factors are proposed. The methods are illustrated by using simulated data.Journal Paper No. J-12733 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 1901     

Archiascomycetes: detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.This work was supported in part by grants 05454030 from the Ministry of Education, Science, and Culture of Japan (to J. S.) and 4369 from the Japan Society for the Promotion of Science Fellowship Programs (to H. N.).     

Inter-specific sequence conservation and intra-individual sequence variation in a spider silk gene

Currently, studies on major ampullate spidroin 1 (MaSp1) genes of non-orb weaving spiders are few, and it is not clear whether genes of these organisms exhibit the same characteristics as those of orb-weavers. In addition, many studies have proposed that MaSp1 might be a single gene with allelic variants, but supporting evidence is still lacking. In this study, we compared partial DNA and amino acid sequences of MaSp1 cloned from different spider guilds. We also cloned partial MaSp1 sequences from genomic DNA and cDNA of the same individuals of spiders using the same primer combination to see if different molecular forms existed. In the repetitive region of partial MaSp1 sequences obtained, GGX, GA and poly-A motifs were present in all Araneomorphae and Mygalomorpae species examined. An extreme similarity in MaSp1 non-repetitive portions was found in sequences of ecribellate, cribellate and Mygalomorphae web-builders and such a result suggested that this sequence might exhibit an important function. A comparison of sequences amplified from the same individual showed that substitutions in amino acids occurred in both repetitive and non-repetitive regions, with a much higher variation in the former. These results suggest that the MaSp1 of Araneomorphae spiders exhibits several forms in an individual spider and it might be either a multiple gene or a single gene with a multiple exon/intron organization.     

Errors of inference in the detection of major gene effects on psychological test scores.

Computer simulation methods were employed to generate abilities of 10 sets of 250 nuclear families, each comprising a pair of randomly mated parents and two children. It was assumed that the distribution of abilities in the population was normal and caused entirely by additive polygenic effects. A simulated psychological test was administered to each sample to generate test scores for each subject. A different test, consisting of 40 items of varying difficulty and discriminating power, was used in each sample. The "mixed model," specifying a single major gene with polygenic and environmental background variation, was tested for each data set. Likelihood ratios were computed to test for the contribution of a major locus and its conformity to Mendelian segregation. Only one out of 10 samples was consistent with pure multifactorial inheritance. Of the remaining nine samples, four showed non-Mendelian segregation and five were consistent with current statistical criteria for establishing the contribution of a major gene to variation in psychological test scores. This high frequency of false conclusions suggests that the naïve application of such methods to behavioral data is often likely to be misleading. Raw test scores alone are not sufficient to test the mixed model. The development of tractable models for behavioral traits requires the responses of subjects to individual items.     

A nonparametric and a parametric version of a test for the detection of the presence of a major gene applicable on data for the complete nuclear family

Summary Nonparametric and parametric tests are suggested for detecting the presence of a major gene for a quantitative trait. The model for the determination of the quantitative trait is an additive one with polygenic, family environment, and individual environment components. The power functions with respect to the major gene effect have been calculated by simulation, and the tests have therefore been compared with each other. The tests have been applied to nuclear family data on human obesity, and the results compared with those obtained using other methods on the same data.This work was done while the author was a visitor at the Istituto di Genetica Biochemica ed Evoluzionistica, CNR, Pavia     

Btl, a structural gene for the major 39–44 kDa amyloplast membrane polypeptides

The aim of the present work was to investigate the relationship between the Btl gene (Btl) and the major 39–44 kDa amyloplast membrane polypeptides which were deficient in amyloplast membranes of brittlel (btl) kernels of maize (Zea mays L.). A rapid yet gentle procedure for the isolation of amyloplasts from immature kernels is described. These amyloplasts were relatively free of contamination by other cellular components, and immunological studies showed that they contained polypeptides which reacted with antibodies to maize starch branching enzyme and ADP-Gle pyrophosphorylase. Purified membranes isolated from the amyloplast contained a poly-peptide which reacted with antibodies to the P_i-translocator from spinach chloroplasts. However, a cluster of 39–44 kDa polypeptides accounted for about 40% of the total amyloplast membrane protein from W64A kernels. These polypeptides were specifically recognized by antibodies raised against a fusion protein consisting of 56 amino acids of the carboxyl terminus of the BTI protein and glutathione S-transferase. The BT1 antibodies also reacted with the abundant polypeptides in amyloplast membranes from hybrid kernels (Doebler 66XP and Pioneer 3780), and the shrunkenl and shrunken2 mutant genotypes, but no BTl reacting polypeptides were present in amyloplast membranes from btl mutant kernels. We were unable to detect BTl by the immunoblot procedure in microsomal membranes from embryo and pericarp tissues from the kernel, from seedling roots and shoots, or in membranes from mitochondria and chloroplasts. The same BTl immunoblot pattern was obtained for proteins extracted from microsomal membranes from developing endosperm and from purified amyloplast membranes. A linear relationship between the number of copies of Btl alleles and the levels of BTl in endosperm microsomal membranes was demonstrated in a gene dosage series. BTl was not extracted from amyloplast membranes by chloroform/methanol or by alkaline buffer at pH 11.5, but was partially extracted by 0.1 M NaOH. These lines of evidence support the conclusion that Btl is the structural gene for the major 39–44 kDa amyloplast membrane polypeptides and that these polypeptides are integral proteins specific to amyloplast membranes from the endosperm.     

Induction of tumour-specific immunity by manipulating the expression of major histocompatibility complex molecules on tumour cells

Abstract Class I major histocompatibility complex (MHC) molecules form part of the target structure recognized by the host cytotoxic T cells (CTL) to reject tumour cells. Many types of malignant tumour cells are reported in which expression of class I MHC genes is down-regulated. By DNA-mediated gene transfer, it is possible to re-express the 'missing' syngeneic (genetically identical) or to introduce 'new' allogeneic (genetically dissimilar) class I MHC genes into these MHC-deficient tumours. In both instances, the immunogenicity of the transfected tumour cells is greatly enhanced and results in their rejection in vivo. More importantly, these 'modified' tumour cells, which are positive for class I MHC molecules, can simultaneously generate an immunity against the 'wildtype' tumour cells which do not express these molecules. These observations suggest the distinct possibility of using gene transfer as a molecular immunotherapeutic approach to abrogate tumour growth.     

A comparison of test statistics for assessing the effects of concomitant variables in survival analysis

In data analysis involving the proportional-hazards regression model due to Cox (1972, Journal of the Royal Statistical Society, Series B 34, 187-220), the test criteria commonly used for assessing the partial contribution to survival of subsets of concomitant variables are the classical likelihood ratio (LR) and Wald statistics. This paper presents an investigation of three other test criteria with potentially major computational advantages over the classical tests, especially for stepwise variable selection in moderate to large data sets. The alternative criteria considered are Rao's efficient score statistic and two other score statistics. Under the Cox model, the performance of these tests is examined empirically and compared with the performance of the LR and Wald statistics. Rao's test performs comparably to the LR test in all the cases considered. The performance of the other criteria is competitive in many cases. The use of these statistics is illustrated in a study of coronary artery disease.     

The Saccharomyces cerevisiae SGE1 gene product: a novel drug-resistance protein within the major facilitator superfamily

Several pleiotropic drug sensitivities have been described in yeast. Some involve the loss of putative drug efflux pumps analogous to mammalian P-glycoproteins, others are caused by defects in sterol synthesis resulting in higher plasma membrane permeability. We have constructed a Saccharomyces cerevisiae strain that exhibits a strong crystal violet-sensitive phenotype. By selecting cells of the supersensitive strain for normal sensitivity after transformation with a wild-type yeast genomic library, a complementing 10-kb DNA fragment was isolated, a 3.4-kb subfragment of which was sufficient for complementation. DNA sequence analysis revealed that the complementing fragment comprised the recently sequenced SGE1 gene, a partial multicopy suppressor of gal11 mutations. The supersensitive strain was found to be a sge1 null mutant. Overexpression of SGE1 on a high-copy-number plasmid increased the resistance of the supersensitive strain. Disruption of SGE1 in a wild-type strain increased the sensitivity of the strain. These features of the SGE1 phenotype, as well as sequence homologies of SGE1 at the amino acid level, confirm that the Sge1 protein is a member of the drug-resistance protein family within the major facilitator superfamily (MFS).