The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP ...hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly ...shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm-Bayesian tool for methylation analysis (Batman)-for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation.
Dalliance is a new genome viewer which offers a high level of interactivity while running within a web browser. All data is fetched using the established distributed annotation system (DAS) protocol, ...making it easy to customize the browser and add extra data.
Dalliance runs entirely within your web browser, and relies on existing DAS server infrastructure. Browsers for several mammalian genomes are available at http://www.biodalliance.org/, and the use of DAS means you can add your own data to these browsers. In addition, the source code (Javascript) is available under the BSD license, and is straightforward to install on your own web server and embed within other documents.
The UK government has recently recognised the need to improve mental health services in the country. Electronic health records provide a rich source of patient data which could help policymakers to ...better understand needs of the service users. The main objective of this study is to unveil statistics of diagnoses recorded in the Case Register of the South London and Maudsley NHS Foundation Trust, one of the largest mental health providers in the UK and Europe serving a source population of over 1.2 million people residing in south London. Based on over 500,000 diagnoses recorded in ICD10 codes for a cohort of approximately 200,000 mental health patients, we established frequency rate of each diagnosis (the ratio of the number of patients for whom a diagnosis has ever been recorded to the number of patients in the entire population who have made contact with mental disorders). We also investigated differences in diagnoses prevalence between subgroups of patients stratified by gender and ethnicity. The most common diagnoses in the considered population were (recurrent) depression (ICD10 codes F32-33; 16.4% of patients), reaction to severe stress and adjustment disorders (F43; 7.1%), mental/behavioural disorders due to use of alcohol (F10; 6.9%), and schizophrenia (F20; 5.6%). We also found many diagnoses which were more likely to be recorded in patients of a certain gender or ethnicity. For example, mood (affective) disorders (F31-F39); neurotic, stress-related and somatoform disorders (F40-F48, except F42); and eating disorders (F50) were more likely to be found in records of female patients, while males were more likely to be diagnosed with mental/behavioural disorders due to psychoactive substance use (F10-F19). Furthermore, mental/behavioural disorders due to use of alcohol and opioids were more likely to be recorded in patients of white ethnicity, and disorders due to use of cannabinoids in those of black ethnicity.
The number of people affected by mental illness is on the increase and with it the burden on health and social care use, as well as the loss of both productivity and quality-adjusted life-years. ...Natural language processing of electronic health records is increasingly used to study mental health conditions and risk behaviours on a large scale. However, narrative notes written by clinicians do not capture first-hand the patients' own experiences, and only record cross-sectional, professional impressions at the point of care. Social media platforms have become a source of 'in the moment' daily exchange, with topics including well-being and mental health. In this study, we analysed posts from the social media platform Reddit and developed classifiers to recognise and classify posts related to mental illness according to 11 disorder themes. Using a neural network and deep learning approach, we could automatically recognise mental illness-related posts in our balenced dataset with an accuracy of 91.08% and select the correct theme with a weighted average accuracy of 71.37%. We believe that these results are a first step in developing methods to characterise large amounts of user-generated content that could support content curation and targeted interventions.
We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA ...methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.
Ensembl 2012 Flicek, Paul; Amode, M. Ridwan; Barrell, Daniel ...
Nucleic acids research,
01/2012, Letnik:
40, Številka:
D1
Journal Article
Recenzirano
Odprti dostop
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and ...zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains ...in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc‐lmb.cam.ac.uk/scop.
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and ...accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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