Tool For Comparative Analysis Research Articles

Mapping the mind of the mobile consumer across borders

PurposeTo define the similarities and differences in perceptions that mobile consumers in culturally distinct markets hold towards the mobile internet.Design/methodology/approachUsing the Zaltman metaphor elicitation technique (ZMET), mental maps between consumers from Indonesia and Japan were developed and compared.FindingsResults showed clear structural similarities between aggregate maps, while differences were found in experiential factors such as technical infrastructure or the underlying business model. The main barriers to widespread consumer adoption of the mobile internet were not found in cognitive structures unique to individual markets, but appeared instead to be caused by inefficiencies within the wireless ecosystem.Research limitations/implicationsThese results identified factors from a number of pre‐existing theories relevant to the mobile platform, suggesting the need to develop a new, more inclusive theory of mobile consumer behavior. ZMET was also shown to be an effective comparative analysis tool applicable to cross‐cultural research.Practical implicationsMarketers can establish sustainable competitive advantage by effectively addressing the many negative aspects consumers raised about the MobileNet. Additionally, these results suggest that the mobile platform can serve as the foundation for truly co‐creative marketing initiatives.Originality/valueThis is the first paper to explore the cognitive structure and content of consumer perceptions of the mobile internet. This study was also the first to apply ZMET as a comparative tool, as well as the first to extend ZMET to include composite weights of construct dyads.

Which Hemochromatosis Mouse Model Is Best for You?: Accessing Information about Mouse Mutant Phenotypes and Their Human Disease Associations.

The mouse is the premier model organism in human disease research because all of its life stages are accessible and there are myriad experimental tools for comparative analysis and specific manipulation of its genome. The Mouse Genome Informatics Database (MGI, http://www.informatics.jax.org ) supports biological knowledge building for the laboratory mouse by integrating and providing access to a wide range of data from DNA sequence to phenotype and disease associations. The integration of complex disease phenotypes, underlying genetic causes, and gene function information can be used to confirm human disease models and provide insight into disease mechanisms. We will illustrate the utility of MGI using hemochromatosis as an example. To describe phenotypic abnormalities and similarities to human disease in the mouse, we developed and utilize a vocabulary of mouse anomalies (the Mammalian Phenotype Ontology) and utilize the human disease terms provided in the Online Mendelian Inheritance in Man (OMIM). These standard terms provide a backbone for annotation, allowing both easy access and searching for researchers via web forms and computational access for data downloads.Within MGI, more than 12,000 mouse mutant alleles have been catalogued, representing mutations in more than 6,150 genes. Of these, more than 1,000 mutant alleles in 760 genes are associated with Mammalian Phenotype terms for hematopoietic defects and approximately 150 of these have an OMIM human disease association. For example, there are 26 alleles in 13 genes associated with Hermansky-Pudlak syndrome, 6 alleles in 4 genes associated with hereditary spherocytosis, and 9 alleles in 5 genes associated with hemochromatosis.According to OMIM data, hemochromatosis in human is associated with at least 5 different genes including HFE, HFE2, HAMP, TFR2, and SLC40A1. In mouse, 12 mutant alleles in three orthologous mouse genes, Hfe, Tfr2, and Slc40a1, have been described and used as potential models for hemochromatosis. Of these mutant alleles, 6 are associated with hemochromatosis phenotypes in MGI. In addition, there are at least 6 mutant alleles in 4 additional genes (B2m, Heph, Tfrc, and Trfr2) that have been associated with the hemocromatosis phenotype in mice and may yet be discovered to influence disease in humans. Finding an appropriate model system for study of human disease is a critical step toward understanding the biological mechanism leading to disease phenotype in human and mouse. MGI provides researchers with query forms that allow simple and complex questions to be addressed. These can range from queries about a single gene or disease term to precise queries that simultaneously address phenotype, disease, gene function, expression, and genome location data. The vocabulary-based phenotype and disease annotations as well as other structured data types can assist in robust and accurate data mining when posing complex biological questions in both computational and individual formats at MGI.

Varieties of Capitalism and Cross-National Gender Differences

The varieties of capitalism (VoC) approach (Hall and Soskice 2001 for an introduction) did not develop as an attempt to explain cross-national gender relations. It was the insight of Estevez-Abe that it could be used in gender analysis (Estevez-Abe this volume). She built on Iversen’s argument that the patterns of business and individual investments in skills implied by VoC could explain complementarities between welfare state regimes and varieties of capitalism (Estevez-Abe et al. 2001; Iversen 2005). These arguments are summarized shortly. This issue of Social Politics shows at least to my reading that VoC offers a range of important insights and tools of comparative analysis; but as Charles points out (this volume) many key characteristics of occupational segregation are common across advanced economies—blue collar work for example is seldom done by women anywhere. VoC is useful then in explaining comparative differences. In this commentary I first sketch out the VoC approach and why it implies that wage determination and skill formation systems differ substantially across economies. Using these two institutional differences the Estevez-Abe argument is set out the links between varieties of capitalism and welfare states are established and a number of implications for cross-national gender differences are drawn. Finally the relation between VoC and political systems are discussed. (excerpt)

GATA: a graphic alignment tool for comparative sequence analysis

BackgroundSeveral problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.ResultsTo address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA ). GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file.ConclusionsGATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA sequences. It provides researchers with a fine-grained alignment and visualization tool aptly suited for non-coding, 0–200 kb, pairwise, sequence analysis. It functions independent of sequence feature ordering or orientation, and readily visualizes both large and small sequence inversions, duplications, and segment shuffling. Since the alignment is visual and does not contain gaps, gene annotation can be added to both sequences to create a thoroughly descriptive picture of DNA conservation that is well suited for comparative sequence analysis.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

BackgroundComparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes.ResultsWe describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at .ConclusionThese tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.

Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system

BackgroundIn this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), or in vitro activated T-cells.ResultsGene clusters, formed based on similarity of expression-pattern across either all tissues or the immune tissues only, had highly significant associations both with immunological processes such as chemokine-mediated response, antigen processing, receptor-related signal transduction, and transcriptional regulation, and also with more general processes such as replication and cell cycle control. Within-cluster gene correlations implicated known associations of known genes, as well as immune process-related roles for poorly described genes. To characterize regulatory mechanisms and cis-elements of genes with similar patterns of expression, we used a new version of a comparative genomics-based cis-element analysis tool to identify clusters of cis-elements with compositional similarity among multiple genes. Several clusters contained genes that shared 5–6 cis-elements that included ETS and zinc-finger binding sites. cis-Elements AP2 EGRF ETSF MAZF SP1F ZF5F and AREB ETSF MZF1 PAX5 STAT were shared in a thymus-expressed set; AP4R E2FF EBOX ETSF MAZF SP1F ZF5F and CREB E2FF MAZF PCAT SP1F STAT cis-clusters occurred in activated T-cells; CEBP CREB NFKB SORY and GATA NKXH OCT1 RBIT occurred in stimulated lymph nodes.ConclusionThis study demonstrates a series of analytic approaches that have allowed the implication of genes and regulatory elements that participate in the differentiation, maintenance, and function of the immune system. Polymorphism or mutation of these could adversely impact immune system functions.

New computational tools for Brassica genome research

With the increasing quantities of Brassica genomic data being entered into the public domain and in preparation for the complete Brassica genome sequencing effort, there is a growing requirement for the structuring and detailed bioinformatic analysis of Brassica genomic information within a user-friendly database. At the Plant Biotechnology Centre, Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data, to aid its application to agricultural biotechnology research. These tools include a sequence database, ASTRA, a sequence processing pipeline incorporating annotation against GenBank, SwissProt and Arabidopsis Gene Ontology (GO) data and tools for molecular marker discovery and comparative genome analysis. All sequences are mined for simple sequence repeat (SSR) molecular markers using ‘SSR primer’ and mapped onto the complete Arabidopsis thaliana genome by sequence comparison. The database may be queried using a text-based search of sequence annotation or GO terms, BLAST comparison against resident sequences, or by the position of candidate orthologues within the Arabidopsis genome. Tools have also been developed and applied to the discovery of single nucleotide polymorphism (SNP) molecular markers and the in silico mapping of Brassica BAC end sequences onto the Arabidopsis genome. Planned extensions to this resource include the integration of gene expression data and the development of an EnsEMBL-based genome viewer.

Phorest: a web‐based tool for comparative analyses of expressed sequence tag data

AbstractComparative analysis of expressed sequence tags is becoming an important tool in molecular ecology for comparing gene expression in organisms grown in certain environments. Additionally, expressed sequence tag database information can be used for the construction of DNA microarrays and for the detection of single nucleotide polymorphisms. For such applications, we present phorest, a web‐based tool for managing, analysing and comparing various collections of expressed sequence tags. It is written in PHP (PHP: Hypertext Preprocessor) and runs on UNIX, Microsoft Windows and Macintosh (Mac OS X) platforms.

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. JASPAR is available at http://jaspar. cgb.ki.se.

The E-Correspondence Principle

We introduce the E-correspondence principle for stochastic dynamic expectations models as a tool for comparative dynamics analysis. The principle is applicable to equilibria that are stable under least squares and closely related learning rules. With this technique it is possible to study, without explicit solving for the equilibrium, how properties of the equilibrium are affected by changes in the structural parameters of the model. Even when qualitative comparative dynamics results are not obtainable, a quantitative version of the principle can be applied.

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.

Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences. A case study using the p53 promoter region of four mammalian species and two fish species is described. Unlike the mammalian sequences the promoter regions in fish have not been previously predicted or characterized and we report the differences in the p53 promoter region of four mammals and that predicted for two fish species. Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/.

Tools for comparative protein structure modeling and analysis.

The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes

IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ®. IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.

Genomic and phylogenetic analysis of the S100A7 (Psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21.

The human S100 gene family encodes the EF-hand superfamily of calcium-binding proteins, with at least 14 family members clustered relatively closely together on chromosome 1q21. We have analyzed the most recently available genomic sequence of the human S100 gene cluster for evidence of tandem gene duplications during primate evolutionary history. The sequences obtained from both GenBank and GoldenPath were analyzed in detail using various comparative sequence analysis tools. We found that of the S100A genes clustered relatively closely together within a genomic region of 260 kb, only the S100A7 (psoriasin) gene region showed evidence of recent duplications. The S100A7 gene duplicated region is composed of three distinct genomic regions, 33, 11, and 31 kb, respectively, that together harbor at least five identifiable S100A7-like genes. Regions 1 and 3 are in opposite orientation to each other, but each region carries two S100A7-like genes separated by an 11-kb intergenic region (region 2) that has only one S100A7-like gene, providing limited sequence resemblance to regions 1 and 3. The duplicated genomic regions 1 and 3 share a number of different retroelements including five Alu subfamily members that serve as molecular clocks. The shared (paralogous) Alu S insertions suggest that regions 1 and 3 were probably duplicated during or after the phase of AluS amplification some 30-40 mya. We used PCR to amplify an indel within intron 1 of the S100A7a and S100A7c genes that gave the same two expected product sizes using 40 human DNA samples and 1 chimpanzee sample, therefore confirming the presence of the region 1 and 3 duplication in these species. Comparative genomic analysis of the other S100 gene members shows no similarity between intergenic regions, suggesting that they diverged long before the emergence of the primates. This view was supported by the phylogenetic analysis of different human S100 proteins including the human S100A7 protein members. The S100A7 protein, also known as psoriasin, has important functions as a mediator and regulator in skin differentiation and disease (psoriasis), in breast cancer, and as a chemotactic factor for inflammatory cells. This is the first report of five copies of the S100A7 gene in the human genome, which may impact on our understanding of the possible dose effects of these genes in inflammation and normal skin development and pathogenesis.

A methodology for automated comparative analysis of metabolite profiling data

Software tools for comparative analysis of metabolite profiling chromatograms have been developed. They include methods for manual and automated correction of retention times and responses by means of corresponding standards. This allows transfer of normalized datasets into databases and, eventually, automated comparison of chromatograms. Chromatogram comparison is based on a univariate peak-by-peak approach using peak heights/areas and corresponding retention times or detector responses and corresponding time points. Tools were developed for comparing single chromatograms to each other. Comparison of multiple chromatograms was achieved by the use of theoretical chromatographic data or theoretical chromatograms calculated from databases as comparators. Results of data analysis may be summarized in graphic as well as in tabular reports listing the number of additional peaks and the magnitudes of (statistically significant) differences.

Operative delivery during labour: trends and predictive factors.

Monitoring operative delivery trends provides the opportunity to consider whether changes are in a direction that will achieve the best outcomes for mothers and their infants. The aims of this study were to identify trends in and predictors of operative delivery (forceps, vacuum or caesarean) among women who have labour; and to determine trends in the operative methods used. The study was based on 616 303 live, singleton, term births delivered between 1990 and 1997 in New South Wales, Australia. There was no change in the annual percentage of women who experienced labour and 20% had an operative birth during labour. The vacuum to forceps ratio declined from 1 : 6 in 1990 to 1 : 1 in 1997. Among women with labour, caesareans increased from 6.4% to 7.8%. For primiparae, the factors predictive of operative delivery (epidural analgesia, age > 34 years, induced or augmented labour and private care) did not change over time. A predictive model for multiparae did not have adequate fit, indicating the importance of data on prior birth history. Studies of trends in operative deliveries are most useful and consistent with decision making when interventions before the onset of labour and during labour are analysed separately. Furthermore, the vacuum:forceps ratio provides a useful tool for comparative analyses.

A comprehensive rice transcript map containing 6591 expressed sequence tag sites.

To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

BackgroundHorizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes.ResultsWe adapted the Maximum Likelihood (ML) mapping to the analyses of all detected quartets of orthologous genes found in four genomes. We have automated the assembly and analyses of these quartets of orthologs given the selection of four genomes. We compared the ML-mapping approach to more rigorous Bayesian probability and Bootstrap mapping techniques. The latter two approaches appear to be more conservative than the ML-mapping approach, but qualitatively all three approaches give equivalent results. All three tools were tested on mitochondrial genomes, which presumably were inherited as a single linkage group.ConclusionsIn some instances of interphylum relationships we find nearly equal numbers of quartets strongly supporting the three possible topologies. In contrast, our analyses of genome quartets containing the cyanobacterium Synechocystis sp. indicate that a large part of the cyanobacterial genome is related to that of low GC Gram positives. Other groups that had been suggested as sister groups to the cyanobacteria contain many fewer genes that group with the Synechocystis orthologs. Interdomain comparisons of genome quartets containing the archaeon Halobacterium sp. revealed that Halobacterium sp. shares more genes with Bacteria that live in the same environment than with Bacteria that are more closely related based on rRNA phylogeny . Many of these genes encode proteins involved in substrate transport and metabolism and in information storage and processing. The performed analyses demonstrate that relationships among prokaryotes cannot be accurately depicted by or inferred from the tree-like evolution of a core of rarely transferred genes; rather prokaryotic genomes are mosaics in which different parts have different evolutionary histories. Probability mapping is a valuable tool to explore the mosaic nature of genomes.

Gender Stratification: A Structural Model for Examining Case Examples of Women in Less-Developed Countries

Feminist social history and theory have produced an array of approaches for the purpose of deconstructing historical records and theoretical frameworks that previously took for granted the second-class status and cultural insignificance of women. However tools for systematic comparative analysis have not been fully integrated into the study of womens place across societies and social classes. A theory of gender stratification based on the work of Rae Lesser Blumberg and Randall Collins offers tools for the systematic and comparative study of women across societies and periods of history. By structural model we mean one that examines the institutional relationships of women and men in the economy politics and the family. This structural/materialist approach has remained in the domain of a relatively small group of sociologists and anthropologists for reasons that are not entirely clear. Blumberg Collins and others have developed theoretical models for the comparative study of gender equality. (excerpt)

The sequence of a 200 kb portion of a Plasmodium vivax chromosome reveals a high degree of conservation with Plasmodium falciparum chromosome 3

Within a 199 866 base pair (bp) portion of a Plasmodium vivax chromosome we identified a conserved linkage group consisting of at least 41 genes homologous to Plasmodium falciparum genes located on chromosome 3. There were no P. vivax homologues of the P. falciparum cytoadherence-linked asexual genes clag 3.2, clag 3.1 and a var C pseudogene found on the P. vivax chromosome. Within the conserved linkage group, the gene order and structure are identical to those of P. falciparum chromosome 3. This conserved linkage group may extend to as many as 190 genes. The subtelomeric regions are different in size and the P. vivax segment contains genes for which no P. falciparum homologues have been identified to date. The size difference of at least 900 kb between the homologous P. vivax chromosome and P. falciparum chromosome 3 is presumably due to a translocation. There is substantial sequence divergence with a much higher guanine+cytosine (G+C) content in the DNA and a preference for amino acids using GC-rich codons in the deduced proteins of P. vivax. This structural conservation of homologous genes and their products combined with sequence divergence at the nucleotide level makes the P. vivax genome a powerful tool for comparative analyses of Plasmodium genomes.