Hypertension 66 (20.3%) 24 (24.2%) 30 (16.3%) NS Diabetes 20 (6.2%) 7 (7.1%) 10 (5.4%) NS Excess weight 78 (24%) 27 (27.3%) 44 (23.9%) NS Smokers 64 (19.7%) 17 (17.2%) 35 (19.0%) NS Age >50 years 137 (42.2%) 54 (54.5%) 67 (36.4%) <0.02 Kidney disease 7 (2.2%) 1 (1%) 5 (2.7%) NS Family history, DM 102 (31.4%) 28 (28.3%) 66 (35.9%) NS

Conflict of interest statement. None declared.

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

/pdf/integrative-analysis-of-the-caenorhabditis-elegans-genome-by-57xztyy5j6.pdf

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein
 interaction data from model organisms and humans
 (http://www.thebiogrid.org). BioGRID currently holds 347 966
 interactions (170 162 genetic, 177 804 protein) curated from both
 high-throughput data sets and individual focused studies, as derived
 from over 23 000 publications in the primary literature. Complete
 coverage of the entire literature is maintained for budding yeast
 (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe)
 and thale cress (Arabidopsis thaliana), and efforts to expand curation
 across multiple metazoan species are underway. The BioGRID houses 48
 831 human protein interactions that have been curated from 10 247
 publications. Current curation drives are focused on particular areas
 of biology to enable insights into conserved networks and pathways that
 are relevant to human health. The BioGRID 3.0 web interface contains
 new search and display features that enable rapid queries across
 multiple data types and sources. An automated Interaction Management
 System (IMS) is used to prioritize, coordinate and track curation
 across international sites and projects. BioGRID provides interaction
 data to several model organism databases, resources such as Entrez-Gene
 and other interaction meta-databases. The entire BioGRID 3.0 data
 collection may be downloaded in multiple file formats, including PSI MI
 XML. Source code for BioGRID 3.0 is freely available without any
 restrictions.

/pdf/the-biogrid-interaction-database-2011-update-4t23jtqdsl.pdf

The BioGRID Interaction Database: 2011 update

Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. Therefore, many groups rely on local bioinformatics support to process queries by accessing the resource's programmatic interfaces if they exist. This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution.

/pdf/biomart-biological-queries-made-easy-382f6c5yr2.pdf

BioMart – biological queries made easy

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.

/pdf/inparanoid-7-new-algorithms-and-tools-for-eukaryotic-3qggzq5uha.pdf

InParanoid 7 : new algorithms and tools for eukaryotic orthology analysis

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.

/pdf/wormbase-a-comprehensive-resource-for-nematode-research-16zpisq8fp.pdf

WormBase: a comprehensive resource for nematode research

WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field.

/pdf/wormbook-the-online-review-of-caenorhabditis-elegans-biology-2q413c2cm8.pdf

WormBook: the online review of Caenorhabditis elegans biology

WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.

/pdf/wormbase-new-content-and-better-access-lspqcu994o.pdf

Michael Han

Papers

WormBase: a comprehensive resource for nematode research

WormBook: the online review of Caenorhabditis elegans biology

WormBase: new content and better access