MetaBase--the wiki-database of biological databases.

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project

Itag2.3 Tomato Genome Annotation, RDF graph

<p>Annotation of the tomato genome, ITAG2.3 (ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/annotation/ITAG2.3_release/). GFF file's were converted into a RDF graph.</p

MQ2 release v1.1.0

<p>Release accompanying publication in Molecular Breeding (http://dx.doi.org/10.1007/s11032-013-9911-3)</p

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source--sink tissues in a segregating potato population

Abstract Background With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. Results Leaf and tuber samples were analysed and screened for the presence of conserved and tissue dependent eQTLs. Expression QTLs present in both tissues are predominantly cis-acting whilst for tissue specific QTLs, the percentage of trans-acting QTLs increases. Tissue dependent eQTLs were assigned to functional classes and visualized in metabolic pathways. We identified a potential regulatory network on chromosome 10 involving genes crucial for maintaining circadian rhythms and controlling clock output genes. In addition, we show that the type of genetic material screened and sampling strategy applied, can have a high impact on the output of genetical genomics studies. Conclusions Identification of tissue dependent regulatory networks based on mapped differential expression not only gives us insight in tissue dependent gene subfunctionalization but brings new insights into key biological processes and delivers targets for future haplotyping and genetic marker development.</p

Additional file 5: Table S5. of Genetical genomics of quality related traits in potato tubers using proteomics

Co-localization of phQTLs (starch, colour and cold sweetening related traits) and pQTLs for proteomics data in 2003. (DOCX 25 kb

Additional file 1: Table S1. of Genetical genomics of quality related traits in potato tubers using proteomics

List of carbohydrate and starch metabolism and cold sweetening related quality traits measured in the CxE population. (DOCX 14 kb

Additional file 2: Table S2. of Genetical genomics of quality related traits in potato tubers using proteomics

pQTL analysis summary for 2002 and 2003 harvest. Number of significant protein QTLs is depicted as well as the chromosomes containing the highest and lowest number of pQTLs. (DOCX 12 kb

Additional file 4: Table S4. of Genetical genomics of quality related traits in potato tubers using proteomics

Co-localization of phQTLs (starch, colour and cold sweetening related traits) and pQTLs for proteomics data in 2002. (DOCX 13 kb