Ensembl Genomes: extending Ensembl across the taxonomic space.

Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Ensembl 2009.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

Estimation of ejection fraction and stroke volume using single- and biplane magnetic resonance imaging of the left cardiac ventricle.

BACKGROUND: In cardiac magnetic resonance imaging (MRI), left ventricular stroke volume (SV) and ejection fractions (EF) are occasionally calculated using single-plane and biplane ellipsoid models. In previous studies, the calculated SV and EF using single- and biplane ellipsoid models have been compared to reference values calculated from short-axis (SA) images. In these studies, however, it has been emphasized that through-plane motion of the basal SA images represents an important source of error, which may result in incorrect reference values. PURPOSE: To compare the calculated SV and EF using single-plane and biplane ellipsoid models with SV and EF calculated from SA images in which compensation was made for through-plane motion. MATERIAL AND METHODS: A group of 20 patients who underwent MRI examination were included in the study. SV and EF were calculated using the stack of SA images (which had been compensated for through-plane motion) and compared to the SV and EF calculated according to the single- and biplane ellipsoid models. RESULTS: The mean difference between the single-plane model and the reference was -0.3+/-6.5 for EF and 7.2+/-17.1 ml for SV. Corresponding comparison between the biplane method and the reference resulted in a mean difference of 0.3+/-6.1 for EF and 11.8+/-14.9 ml for SV. CONCLUSION: The results from this study show that left ventricular EF can be adequately estimated using the single- and biplane ellipsoid models, while SV tends to be overestimated using both geometrical models.

Ensembl 2008.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Outer contour and radial changes of the cardiac left ventricle: a magnetic resonance imaging study.

Earlier studies have shown a +/-5% end-systolic decrease in the volume encompassed by the pericardial sack, manifesting as a radial diminution of the pericardial/epicardial contour of the left ventricle (LV). The aim of this study was to measure this radial displacement at different segmental levels of the LV and try to find out were it is as greatest and to calculate regional myocardial volume changes as a reference in healthy subjects. Eleven healthy subjects were examined by magnetic resonance imaging. Images were acquired using an ECG-triggered balanced fast field echo pulse sequence. The epicardial borders of the LV wall were delineated in end-diastole (ED) and end-systole (ES). Regional changes of the LV wall were analysed at three different levels (base, mid and apex) by dividing the myocardium into segments. The volumes obtained as the differences between the outer volume of the left ventricle at ED and ES at different slice levels were found to be greatest at the base of the heart and lowest at apex. The relative inward motion, that is the motion in short-axis direction of the epicardial border of the myocardium from ED to ES towards the centre of the LV, was greatest at the base and lowest at the mid level, something that has to be taken into account when measuring the LV during clinical exams. There was a significant difference in the relative inward motion between the segments at apex (p < 0.0001), mid (p = 0.036) and at base level (p < 0.0001).

Ensembl 2007.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Ensembl 2006.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Ensembl 2005.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Ensembl 2004.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

Comparison between circumflex artery motion and mitral annulus motion.

OBJECTIVE: To compare mitral annulus motion (MAM) with circumflex artery motion (CXM) and the motion amplitude at an endocardial site (representing MAM) with an epicardial site (representing CXM) at the most basal lateral part of the atrioventricular plane (AVP). DESIGN: MAM and CXM were obtained in 28 patients examined by echocardiography and coronary angiography. The motion amplitude epicardially and endocardially was recorded by echocardiography in 13 patients with normal ejection fraction (EF) (> or = 0.50) and in 13 patients with decreased EF (<0.50). RESULTS: CXM was higher than MAM in most patients with normal EF but lower than MAM in most patients with decreased EF. The motion amplitude epicardially was significantly higher (p < 0.001) than endocardially in patients with normal EF. while there was no significant difference in patients with decreased EF. CONCLUSION: CXM represents the motion of the epicardial part of the AVP and differs from MAM, which represents the endocardial part of the wall. This must be considered when CXM is used for assessment of left ventricular systolic function.

Usefulness of coronary angiography for assessing left ventricular function.

The correlation of ejection fraction to left ventricular long-axis contractions, measured from left coronary ostium to apical arterial branches, on coronary angiograms was investigated.