CIPRO 2.5

Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

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

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includesoriginal large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite ofdevelopmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and geneexpression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analysesat various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a communitysupported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http:// cipro.ibio.jp/2.5.

Original languageEnglish
JournalNucleic Acids Research
Volume39
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 2011 Jan

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Ciona intestinalis
Protein Databases
Computational Biology
Databases
Molecular Sequence Annotation
Urochordata
Electrophoresis, Gel, Two-Dimensional
Ciprofloxacin
Proteomics
Vertebrates
Biomedical Research
Mass Spectrometry
Proteins
Genome
Research

ASJC Scopus subject areas

  • Genetics

Cite this

CIPRO 2.5 : Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. / Endo, Toshinori; Ueno, Keisuke; Yonezawa, Kouki; Mineta, Katsuhiko; Hotta, Kohji; Satou, Yutaka; Yamada, Lixy; Ogasawara, Michio; Takahashi, Hiroki; Nakajima, Ayako; Nakachi, Mia; Nomura, Mamoru; Yaguchi, Junko; Sasakura, Yasunori; Yamasaki, Chisato; Sera, Miho; Yoshizawa, Akiyasu C.; Imanishi, Tadashi; Taniguchi, Hisaaki; Inaba, Kazuo.

In: Nucleic Acids Research, Vol. 39, No. SUPPL. 1, 01.2011.

Research output: Contribution to journalArticle

Endo, T, Ueno, K, Yonezawa, K, Mineta, K, Hotta, K, Satou, Y, Yamada, L, Ogasawara, M, Takahashi, H, Nakajima, A, Nakachi, M, Nomura, M, Yaguchi, J, Sasakura, Y, Yamasaki, C, Sera, M, Yoshizawa, AC, Imanishi, T, Taniguchi, H & Inaba, K 2011, 'CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality', Nucleic Acids Research, vol. 39, no. SUPPL. 1. https://doi.org/10.1093/nar/gkq1144
Endo, Toshinori ; Ueno, Keisuke ; Yonezawa, Kouki ; Mineta, Katsuhiko ; Hotta, Kohji ; Satou, Yutaka ; Yamada, Lixy ; Ogasawara, Michio ; Takahashi, Hiroki ; Nakajima, Ayako ; Nakachi, Mia ; Nomura, Mamoru ; Yaguchi, Junko ; Sasakura, Yasunori ; Yamasaki, Chisato ; Sera, Miho ; Yoshizawa, Akiyasu C. ; Imanishi, Tadashi ; Taniguchi, Hisaaki ; Inaba, Kazuo. / CIPRO 2.5 : Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. In: Nucleic Acids Research. 2011 ; Vol. 39, No. SUPPL. 1.
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abstract = "The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includesoriginal large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite ofdevelopmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and geneexpression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analysesat various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a communitysupported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http:// cipro.ibio.jp/2.5.",
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AU - Mineta, Katsuhiko

AU - Hotta, Kohji

AU - Satou, Yutaka

AU - Yamada, Lixy

AU - Ogasawara, Michio

AU - Takahashi, Hiroki

AU - Nakajima, Ayako

AU - Nakachi, Mia

AU - Nomura, Mamoru

AU - Yaguchi, Junko

AU - Sasakura, Yasunori

AU - Yamasaki, Chisato

AU - Sera, Miho

AU - Yoshizawa, Akiyasu C.

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