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Here we present Translocatome, the first dedicated database of human translocating proteins (
http://translocatome.linkgroup.hu). The core of the Translocatome database is the manually curated data set of 213 human translocating proteins listing the source of their experimental validation, several details of their translocation mechanism, their local compartmentalized interactome, as well as their involvement in signalling pathways and disease development. In addition, using the well-established and widely used gradient boosting machine learning tool, XGBoost, Translocatome provides translocation probability values for 13 066 human proteins identifying 1133 and 3268 high- and low-confidence translocating proteins, respectively. The database has user-friendly search options with a UniProt autocomplete quick search and advanced search for proteins filtered by their localization, UniProt identifiers, translocation likelihood or data complexity. Download options of search results, manually curated and predicted translocating protein sets are available on its website. The update of the database is helped by its manual curation framework and connection to the previously published ComPPI compartmentalized protein-protein interaction database (http://comppi.linkgroup.hu). As shown by the application examples of merlin (NF2) and tumor protein 63 (TP63) Translocatome allows a better comprehension of protein translocation as a systems biology phenomenon and can be used as a discovery-tool in the protein translocation field.
This article was published in the following journal.
Name: Nucleic acids research
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The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
Translation products of a fusion gene derived from CHROMOSOMAL TRANSLOCATION of C-ABL GENES to the genetic locus of the breakpoint cluster region gene on chromosome 22. The p210(bcr-abl) fusion protein is found in patients with LEUKEMIA, MYELOGENOUS, CHRONIC, BCR-ABL POSITIVE. The p190(bcr-abl) fusion protein is found in patients with PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA. The activation of human c-abl by chromosomal translocation is essentially the same as the activation of murine c-abl by viral translocation in ABELSON MURINE LEUKEMIA VIRUS.
A scanning microscope-based, cytofluorimetry technique for making fluorescence measurements and topographic analysis on individual cells. Lasers are used to excite fluorochromes in labeled cellular specimens. Fluorescence is detected in multiple discrete wavelengths and the locational data is processed to quantitatively assess APOPTOSIS; PLOIDIES; cell proliferation; GENE EXPRESSION; PROTEIN TRANSPORT; and other cellular processes.
A 1.5-kDa small ubiquitin-related modifier protein that can covalently bind via an isopeptide link to a number of cellular proteins. It may play a role in intracellular protein transport and a number of other cellular processes.
Multiprotein complexes that carry out PROTEIN TRANSPORT across CELL MEMBRANES.
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