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For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of _Ciona intestinalis_, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for _Ciona_ proteins.  In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta _et al_., and cross-references with JGI version 1 and ENSEMBL.  A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database.  The information is summarized in a single page for a protein.  Together with BLAST results, comparative genomics, expression profiles, domain search results, localization, phylogeny etc., we provide biologists the highly integrated view amongst the existing databases, which facilitates to understand the protein.  For example, the 2D-PAGE and the microarray results of the same protein are sometimes different, which implies the spatial or temporal gaps of the expressions between the mRNA and the protein.  Besides, two functionalities are implemented.  One is an improved 2D-PAGE viewer, which provides the compact view of spots and experimental information, and another is peptide fragment mass search functionality as improved PerMS algorithm by Hozumi _et al_., by enabling detection of seven kinds of modifications and suspected contaminants

Integral presentation of Experimental Results and Bioinformatic Analyses on Ciona intestinalis Proteins