The holidays have come a little early for epigeneticists! Nucleic Acids Research just published papers on several databases that put a wealth of information on various epi-phenomena right at your fingertips. Chances are, at least one of these has info that will make your research life a whole lot easier.
The Histone Infobase (HIstome), or “knowledgebase,” is a browsable, manually curated, relational database that houses all the “411” on human histones, including modification sites, variants, and the enzymes that modify them. The web-based resource presents these data (on 55 histones, 106 PTM sites, and 152 modifying enzymes) in an easily accessible format. For example, the entries are grouped into several logical categories. External links take you to information in other public databases. HIstome is freely available.
Wondering if your favorite gene is methylated in the brain? Look no further than MethylomeDB, a new brain methylome database that provides genome-wide human and mouse brain DNA methylation profiles. The profiles cover more than 80% of brain CpGs at single-CpG resolution. Profiles from control, schizophrenia, and depression samples are included. Data from the authors and from other research groups are in this database, and users can download data for individual samples. Because it contains human and mouse data, cross-species comparisons are possible. The researchers say that this is the “first source of comprehensive brain methylome data.” Visit MethylomeDB
This DNA methylation database focuses on human diseases. DiseaseMeth has more than 14,000 entries from over 25,000 published papers and 175 high-throughput methylation data sets for 50 diseases from various websites and institutes. To date, DiseaseMeth includes data on 72 human diseases generated by many different methods. The database also includes several reference data sets from normal tissues and cells that users can compare with the disease data to identify differentially methylated genes and make new discoveries about gene-disease relationships. Check out DiseaseMeth.
It seems that we’re being flooded with miRNA targets these days. So, it’s not too surprising that databases compiling this info are coming onto the scene. One of those databases is TarBase 6.0—it provides data on miRNA targets generated using all kinds of methods and includes powerful data analysis tools in an easy-to-use format. For each miRNA-gene interaction, there are data on each specific miRNA and gene, as well as validation info. The researchers say that this is the “largest collection of manually curated experimentally validated miRNA-gene interactions (more than 65,000 targets), presenting a 16.5-175-fold increase over other available manually curated databases.” Sounds pretty impressive. See TarBase 6.0 for yourself.
We’ve also noticed a lot of papers on long noncoding RNAs (lncRNAs) recently. To help epigeneticists deal with all this info, researchers have updated the NONCODE database to include lncRNAs. The database now includes expressional and functional lncRNA data from re-annotated microarray studies—all in one place. NONCODE now has 411,552 entries, more than double the number of entries included in v2.0. The easy-to-use web interface provides several search and browse options. Just discovered a new lncRNA? You can submit it to the database via a submission system. NONCODE v3.0 is freely available.
miRNEST is a database that integrates info on miRNAs from animals, plants, and viruses and puts it all together in one location with a uniform format for easy use. The web interface is user-friendly and allows researchers to sift through data on miRNAs in 544 species. The data include those that the authors generated by using animal and plant ESTs from dbEST. That’s how they got 10,004 of the miRNA candidates—even candidates for 236 species for which no miRNAs were previously known. They also added info from three other databases, two published papers, and 12 other resources. A total of 39,122 miRNAs are in miRNEST—enough to keep you busy at least until New Year’s.