ArkMAP: integrating genomic maps across species and data sources.

BACKGROUND: The visualisation of genetic and genomic maps aligned within and between species and across data sources can be used to inform studies of genome evolution, assist genome assembly projects and aid gene discovery and identification. Whilst annotation, integration and exploration of assembled genome sequences is well supported, there are fewer tools available which can display genetic maps for less well-characterized species, and integrate these maps with annotated reference genomes to support cross species comparisons. RESULTS: We have developed a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics. CONCLUSIONS: ArkMAP allows users to draw and interactively explore gene and variation maps for any version of any annotated genome curated in the Ensembl data sources, and to integrate local mapping data. The maps and inter-map relationships drawn are highly configurable and ArkMAP may be used to produce publication quality graphics. ArkMAP is freely available as an auto-updating Java 'Web Start' application, or as a standalone archived application.

JEnsembl: a version-aware Java API to Ensembl data systems.

MOTIVATION: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. RESULTS: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. AVAILABILITY: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.

BACKGROUND: Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure. METHODS AND RESULTS: This paper describes an evaluation of how VIPER displays the different scales and types of dataset that occur experimentally, with a description of how VIPER's display interface and functionality meet the challenges presented by such data. We examine a range of possible error types found in real and simulated pedigree genotype datasets, demonstrating how these errors are exposed and explored using the VIPER interface and we evaluate the utility and usability of the interface to the domain expert.Evaluation was performed as a two stage process with the assistance of domain experts (geneticists). The initial evaluation drove the iterative implementation of further features in the software prototype, as required by the users, prior to a final functional evaluation of the pedigree display for exploring the various error types, data scales and structures. CONCLUSIONS: The VIPER display was shown to effectively expose the range of errors found in experimental genotyped pedigrees, allowing users to explore the underlying causes of reported inheritance inconsistencies. This interface will provide the basis for a full data cleaning tool that will allow the user to remove isolated bad data points, and reversibly test the effect of removing suspect genotypes and pedigree relationships.

Deletion of Serpina1a, a murine α1-antitrypsin ortholog, results in embryonic lethality.

Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States Approximately 1% to 2% of COPD patients suffer from α(1)-antitrypsin (A1AT) deficiency, the major inheritable predisposition to COPD/emphysema. To further study the role of A1AT deficiency in the pathogenesis of COPD/emphysema, the authors attempted to generate null-mutant mice for Serpina1a, 1 of 2 A1AT orthologs in mice. Here the authors show that targeted deletion of Serpina1a results in embryonic lethality prior to 8.5 days post conception (dpc). The results are surprising given that A1AT-null humans exist and therefore do not require this gene product for normal development. The Serpina1 gene cluster is substantially different between mouse and man. Through gene duplication, mice have 3 to 5 (depending on the strain) highly homologous proteinase inhibiting (Pi) genes, 2 of which inhibit neutrophil elastase. Despite the abundance of Pi genes in mice, Serpina1a serves a critical, nonredundant function during early mouse development. A1AT-deficient mice have been highly sought after to study emphysema, cancer, and liver disease, and as a model to perfect gene replacement therapy. These results highlight important differences between human and murine serpins and point to the difficulty inherent to using gene-targeted mice to study this common human genetic disease.

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

BACKGROUND: Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner. RESULTS: We have developed a simple generic XML schema (GenomicMappingData.xsd - GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows. CONCLUSION: The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

A proximal E-box modulates NGF effects on rat PPT-A promoter activity in cultured dorsal root ganglia neurones.

The rat preprotachykinin A (rtPPTA) promoter fragment spanning -865+92, relative to the major transcriptional start, has previously been demonstrated to be nerve growth factor (NGF) responsive in primary cultures of rat dorsal root ganglion (DRG) neurones [Harrison, P.T., Dalziel, R.G., Ditchfield, N.A., Quinn, J.P., 1999. Neuronal-specific and nerve growth factor-inducible expression directed by the preprotachykinin-A promoter delivered by an adeno-associated virus vector. Neuroscience 94, 997-1003]. In this communication, we demonstrate that an E box element at -60, in part, regulates the activity of this rtPPT-A promoter fragment in DRG neurones in response to NGF. Differential regulation of the promoter is observed in the presence or absence of NGF when the E Box site is present. Under basal conditions binding of proteins to this -60 element may antagonise promoter activity. Hence, in the absence of NGF, mutation of the -60 E box increased reporter gene expression. Further, comparison of levels of reporter gene expression supported by both WT and mutated promoter indicate that in the presence of NGF the -60 E box element also plays a role as an activator domain. This represents a novel mechanism for NGF regulation of rtPPT-A. Similarly, an important role for this signalling pathway was observed in neonate rat DRG neuronal cultures, which require NGF for their survival, namely mutation of the -60 element resulted in higher levels of reporter gene expression.