CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

Lixy Yamada,Kohji Hotta,Michio Ogasawara,Yutaka Satou,Tadashi Imanishi,Junko Yaguchi,Mia Nakachi,Katsuhiko Mineta,Kazuo Inaba,Miho Sera,Ayako Nakajima,Hiroki Takahashi,Alu Konno,Toshinori Endo,Chisato Yamasaki,Sasakura Yasunori,Mamoru Nomura,Koji Ueno ,Hiroyuki Taniguchi ,Akiyasu C Yoshizawa ,Kazuya Yonezawa

doi:10.1038/npre.2010.5435.1

Abstract

AbstractCIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics.

Highlights

CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata
The current database contains 89,683 unique sequences covering all the proteins from all the gene models on this species; the number was reduced to 70,493 by similarity clustering. these sequences, more than 5,000 proteins are manually annotated based on the large-scale transcriptomic, proteomic and bioinformatic data. annotations can be subjected to be qualification by rating, curation, and comments by named and anonymous users through the web site of CIPRO database. views are shown in figures 1 and 2
Whole Ciona intestinalis proteome database Proteins across gene models are presented: all protein models derived from published gene models are incorporated, including Kyoto model (KG), KH, PROCITS, JGI's versions 1 and 2, and Ensembl are incorporated

Summary

Whole Ciona intestinalis proteome database

Proteins across gene models are presented: all protein models derived from published gene models are incorporated, including Kyoto model (KG), KH (successor of KG model), PROCITS, JGI's versions 1 and 2, and Ensembl (version 58.2) are incorporated.

Original comprehensive user-friendly interfaces

Community-wide curation capability opened to users

Experimental assistance information