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RPFdb (Ribosome profiling footprinting database)

Translational control is crucial in the regulation of gene expression and deregulation of translation is associated with a wide range of cancers and human diseases. Ribosome profiling is a technique that provides genome wide information of mRNA in translation based on deep sequencing of ribosome protected mRNA fragments (RPF). RPFdb is a comprehensive resource for hosting, analyzing and visualizing RPF data. The current version of database contains 777 samples from 82 studies in 8 species, processed and reanalyzed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. (I) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; (II) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; (III) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. Overall the database provides a simple way to search, analyze, compare, visualize and download RPF data sets.
http://www.rpfdb.org
http://sysbio.sysu.edu.cn/rpfdb/

hPDI (Human Protein-DNA Interaction database)

The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human TFs but also for more than 500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search, and download a subset or the entire data via a web interface. This database is freely accessible for academic purposes.
http://bioinfo.wilmer.jhu.edu/PDI/

 
 
 
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