SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum.
BACKGROUND
Schistosoma japonicum is one of the three major blood fluke species, the etiological agents of schistosomiasis which remains a serious public health problem with an estimated 200 million people infected in 76 countries. In recent years, enormous amounts of both transcriptomic and proteomic data of schistosomes have become available, providing information on gene expression profiles for developmental stages and tissues of S. japonicum. Here, we establish a public searchable database, termed SjTPdb, with integrated transcriptomic and proteomic data of S. japonicum, to enable more efficient access and utility of these data and to facilitate the study of schistosome biology, physiology and evolution.


METHODS
All the available ESTs, EST clusters, and the proteomic dataset of S. japonicum are deposited in SjTPdb. The core of the database is the 8,420 S. japonicum proteins translated from the EST clusters, which are well annotated for sequence similarity, structural features, functional ontology, genomic variations and expression patterns across developmental stages and tissues including the tegument and eggshell of this flatworm. The data can be queried by simple text search, BLAST search, search based on developmental stage of the life cycle, and an integrated search for more specific information. A PHP-based web interface allows users to browse and query SjTPdb, and moreover to switch to external databases by the following embedded links.


CONCLUSIONS
SjTPdb is the first schistosome database with detailed annotations for schistosome proteins. It is also the first integrated database of both transcriptome and proteome of S. japonicum, providing a comprehensive data resource and research platform to facilitate functional genomics of schistosome. SjTPdb is available from URL: http://function.chgc.sh.cn/sj-proteome/index.htm.
Liu
Feng
F
Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, PR China. liuf@chgc.sh.cn
Chen
Ping
P
Cui
Shu-Jian
SJ
Wang
Zhi-Qin
ZQ
Han
Ze-Guang
ZG
D000818:Animals; D020451:Contig Mapping; D018509:DNA, Helminth / Q000235:genetics*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D023281:Genomics; D015801:Helminth Proteins / Q000235:genetics*; D040901:Proteomics; D012549:Schistosoma japonicum / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
D018509:DNA, Helminth; D015801:Helminth Proteins