Sys-BodyFluid: a systematical database for human body fluid proteome research

Abstract

Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.

Figure 1.

The web graphical user interface of Sys-BodyFluid database. (A) Search part and option. Users could search protein by protein ID, protein name and sequence similarity. (B) Browse part. Database allows user browse protein by their interested body fluid and interested paper. Protein existed in two body fluids could also be viewed and multi body fluids can be investigated. (C) Protein annotation part. There is detailed information in the database for each protein, including description, domain, Gene Ontology term, sequence and so on. (D) Pathway part. The proteins (colored by red) in different body fluids and their involved pathway are shown in pathway link. Proteins in our database are labeled with ‘red’ color. The body fluid number and paper number are also showed in the web page.

Figure 2.

(A) The data comparison in different body fluids. There are 2928 proteins presented in at least two body fluids and 1359 proteins existed in at least three body fluids. Only 15 proteins exist in total 11 body fluids. (B) Gene Ontology annotation statistical analysis for the 2928 proteins existing in at least two body fluids.