title: OrysPSSP: a comparative platform for small secreted proteins from rice and other plants.
abstract: Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had not been any effort to systematically analyze rice SSPs. Here, we constructed a comparative platform, OrysPSSP (http://www.genoportal.org/PSSP/index.do), involving >100 000 SSPs from rice and 25 plant species. OrysPSSP is composed of a core SSP database and a dynamic web interface that integrates a variety of user tools and resources. The current release (v0530) of core SSP database contains a total of 101 048 predicted SSPs, which were generated through a rigid computation/curation pipeline. The web interface consists of eight different modules, providing users with rich resources/functions, e.g. browsing SSP by chromosome, searching and filtering SSP, validating SSP with omics data, comparing SSP among multiple species and querying core SSP database with BLAST. Some cases of application are discussed to demonstrate the utility of OrysPSSP. OrysPSSP serves as a comprehensive resource to explore SSP on the genome scale and across the phylogeny of plant species.
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Bohu
authors.initials: B
authors.lastname: Pan
authors.forename: Jia
authors.initials: J
authors.lastname: Sheng
authors.forename: Weining
authors.initials: W
authors.lastname: Sun
authors.forename: Yinhong
authors.initials: Y
authors.lastname: Zhao
authors.forename: Pei
authors.initials: P
authors.lastname: Hao
authors.forename: Xuan
authors.initials: X
authors.lastname: Li
mesh_terms: D030562:Databases, Protein; D023281:Genomics; D020407:Internet; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D055571:Secretory Pathway; D012984:Software; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins