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UniProt release 9.3

Published December 12, 2006

Headlines

Major update of a re-emerging pathogen: Dengue virus.

Dengue is a mosquito-borne virus found in tropical and sub-tropical regions around the world, predominantly in urban and semi-urban areas in south-east Asia, Africa, and South America.

During the 1970s, the disease had become sporadic due to an active vector control program. Moreover since the 1980s, both the virus and his vector have re-emerged and spread even wider than before: the disease is now found in more than 100 countries. The reasons for this re-emergence probably include the growing extension of urban areas and the suspension of the vector control program.

The virus is transmitted to humans through the bite of an infected Aedes aegypti mosquito and subsequently replicates in skin dendritic cells before infecting lymph nodes and blood cells. The symptoms are fever and pain, that can be sustained for up to 7 days. In rare cases, human infection leads to dengue haemorrhagic fever (DHF), a potentially fatal complication. Today, DHF affects most Asian countries and has become a leading cause of hospitalisation and death among children.

Some 2500 million people -- two fifths of the world's population -- are now at risk from dengue. WHO currently estimates there may be 50 million cases of dengue infection worldwide every year. The mild autumn of 2006 has favoured the spread of the vector and has been responsible for a major outbreak of dengue in India, with many reported cases in New Delhi.

The growing number of dengue virus sequences ( currently over 3400 in UniProtKB/TrEMBL ) and the absence of taxonomic nomenclature complicates the identification of medical samples.

In the current UniProtKB/Swiss-Prot release, we have adopted a systematic nomenclature for 28 representative dengue strains, where we indicate the country and the year of isolation besides the strain name.

Example: Dengue virus type 2 (strain TH-36)
becomes: Dengue virus type 2 (strain Thailand/TH-36/1958)

The virus (+)RNA genome codes for a single polyprotein, cleaved in more than 12 products. 32 representative dengue virus polyproteins have been annotated and are available in UniProtKB/Swiss-Prot. (ex: P33478)


UniProtKB News

Protein Spotlight document

Protein Spotlight (ISSN 1424-4721 - http://www.expasy.org/spotlight/) is a monthly review written by the Swiss-Prot team of the SIB Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.

The protsprot document lists for each Protein Spotlight article the corresponding UniProtKB/Swiss-Prot entries that it cites.

Cross-references to DIP

Cross-references have been added to the Database of interacting proteins. The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.

The DIP is available at http://dip.doe-mbi.ucla.edu/.

The format of the explicit links in the flat file is:

Resource abbreviation DIP
Resource identifier DIP accession number.
Examples 
Q9W1K5:
DR   DIP; DIP:19601N; -.

P41597:
DR   DIP; DIP:5833N; -.
DR   DIP; DIP:5839N; -.

Cross-references to Reactome

The resource identifier of the cross-references to the Reactome database has been modified. The resource identifier was a Reactome unique identifier for a protein, which was identical to the Swiss-Prot primary AC number of that protein. Now it is a stable Reactome identifier. In addition, the pathway name is given as an optional information field.

Resource identifier Reactome identifier.
Optional information 1 Pathway name.
Examples 
P61978:
DR   Reactome; REACT_1675.1; mRNA Processing.
DR   Reactome; REACT_71.1; Gene Expression.

P62191:
DR   Reactome; REACT_152.2; Cell Cycle, Mitotic.
DR   Reactome; REACT_1538.1; Cell Cycle Checkpoints.
DR   Reactome; REACT_383.2; DNA Replication.
DR   Reactome; REACT_6185.3; HIV Infection.
DR   Reactome; REACT_6850.1; Cdc20:Phospho-APC/C mediated degradation of Cyclin A.

Cross-references to GermOnline

The resource identifier of the cross-references to the GermOnline database has been modified. The resource identifier was a GermOnline identifier for a gene. Now it is a gene identifier from any source, e.g. Ensembl or model organism database. In addition, the organism name is is given as an optional information field.

Resource identifier Gene identifier from any source, e.g. Ensembl or model organism database.
Optional information 1 Organism name.
Examples 
P02766:
DR   GermOnline; ENSG00000118271; Homo sapiens.

P32559:
DR   GermOnline; YMR023C; Saccharomyces cerevisiae.

Changes concerning keywords

New keyword:

Modified keywords: