CIPRO 2.5:?Ciona intestinalis?Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments

摘要

CIPRO database (http://cipro.ibio.jp/2.5) is an integratedprotein database for a tunicate species Ciona intestinalisthat is part of the Urochordata. Although CIPRO pro-vides proteomic and transcriptomic data on a single spe-cies, the animal is considered unique in the evolutionarytree, representing a possible origin of the vertebratesand is a good model for understanding chordate evolu-tion, including human evolution. Furthermore, C. intes-tinalis has been one of the favorites of developmentalbiologists; therefore, a lot of amount of accumulatedknowledge on its development, morphology, in additionto the recent genome sequence and gene expressiondata exists. The CIPRO database aims to collect pub-lished data and to present unique information, includingthe unpublished transcriptomic and proteomic data andhuman curated annotation, for the use of researchers inbiology and bioinformatics. The current database con-tains 89,673 unique sequences covering all the proteinsfrom all the gene models on this species; the numberwas reduced to 70,493 by similarity clustering. Of thesesequences, more than 5,000 proteins are manually anno-tated based on the large-scale transcriptomic, proteomicand bioinformatic data. Those annotations can be sub-jected to be qualification by rating, curation, andcomments by named and anonymous users through theweb site of CIPRO database. Unique features of CIPROdatabase include:(i) Original experimental data Unpublished experi-mental data, including 2D-PAGE with the identifiedprotein spots by protein mass fingerprint (PMF) MSanalysis, expressions or localizations of protein andRNA across developmental stages and tissues, altogethersummarized in a single chart for the comparison amongstatus and methods. RNA expressions are observed bymicroarray and EST. Each protein is linked to an inde-pendent Ascidian Proteome Database summarizinglarge-scale MS-based proteomic analyses.(ii) Whole Ciona intestinalis proteome databaseProteins across gene models are presented: all proteinmodels derived from published gene models are incor-porated, including Kyoto model (KG), KH (successor ofKG model), PROCITS, JGI's versions 1 and 2, andEnsembl (version 58.2) are incorporated. Identicalsequences across gene models are shown.(iii) Original comprehensive user-friendly interfacesBioinformatic analyses and prediction results are sum-marized in pictures for grasp at a glance: homologysearch, cytolocalization, secondary structure predictioncombined with modification sites, such include phos-1phorylation and three-dimensional structures.