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).
Gathers information about the protein-coding genes of seventeen major cancer types and their genome-wide transcriptome. Pathology Atlas is an open-access database, part of the Human Protein Atlas, which aims to examine the prognostic role of each protein-coding gene in the different cancers. The database uses transcriptomics and antibody-based profiling to provide a standalone resource for cancer precision medicine.
Provides access to the genomic alignments of public ribo-seq reads in conjunction with mRNA-seq reads along with relevant annotation tracks. GWIPS-viz is a specialized ribo-seq browser allowing researchers to support ribo-seq evidence for alternative proteoforms inferred from phylogenetic analysis or detect with proteomics or other experimental techniques. It can be used as a support tool for predictions based on other approaches and for generating hypotheses that can be tested using methods other than ribo-seq.
Allows to identify short open reading frames (sORFS). SORFS.org presents two interfaces: (1) the default query interface provides real-time lookup of sORFs with limited query possibilities and (2) a BioMart query interface was developed enabling advanced query and export options. This database contains more than 260 000 sORFs. This detail page also contains a RIBO-seq visualization tool, permitting manual inspection of RIBOseq data. This extensive platform can help researchers with limited bioinformatics knowledge in sORFS domain.
A comprehensive resource for hosting, analyzing and visualizing ribosome protected mRNA fragment (RPF) data. RPFdb 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.
Collects the RNC-seq, Ribo-seq and the corresponding mRNA-seq data from Gene Expression Omnibus (GEO) and Short Read Archive (SRA) databases. TranslatomeDB is an online resource that offers differential gene expression (DGE) analysis to compare two datasets and calculates translation ratios (TR) and elongation velocity index (EVI) to quantitatively assess the translation initiation efficiency and elongation speed.
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