RPD
2016/02/02Web Site: http://gene64.dna.affrc.go.jp/RPD/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rpd/
The information on proteins identified from several organs and organelles of rice on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) reference maps.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "RPD" data. |
| File | README_e.html(English) |
2.2 Gel table
| Data name | Gel table |
| Description of data contents | List of gel image of 2D-PAGE for various organ or organelle in rice. |
| File | rpd_main.zip (1 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Tissue ID | ID of the 2D-PAGE image. |
| Tissue type | Type of organ column. "tissue": growing stage or kind of organ. "organelle": kind of organelle. |
| Tissue | Kind of organ or organelle. |
| Gel image | File name of gel image. |
| Spot No gel image | File name of gel image with spot No. |
2.3 Spot table
| Data name | Spot table |
| Description of data contents | List of the spots obtained by 2D-PAGE. The information for each spot such as Mw, pI, expression level, the amino acid sequence, and the result of homology search is provided. |
| File | rpd_spot.zip (326 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Spot ID | ID of the spot. |
| Spot No. | Serial number of this spot on the gel. |
| tissue ID | ID of the 2D-PAGE image. |
| pI | pI (isoelectric point) of protein on this spot. |
| MW | MW (molecular weight) of protein on this spot. |
| organism | Plant material that user for protein extraction. |
| tissue | Tissue or organella for extracting tissue material. |
| expression | Expression of protein analysed by 2D ELITE (image analysis software of two-dimensional polyacrylamide gel electrophoresis, Amersham). |
| spot gel image | Extended gel image of the spot. |
| Mass Spectrometry Accession No. | Accession No. of homologous protein by Mascot Analysis. |
| Mass Spectrometry Homologous Protein | Definition of homologous protein by Mascot Analysis. |
| Mass Spectrometry Score (%) | Mascot score. |
| Protein Sequencer Accession No. | Accession No. of homologous protein by protein sequencer. (multiple entries) |
| Protein Sequencer Homologous Protein | Definition of homologous protein by Mascot Analysis. (multiple entries) |
| cDNA Accession No. | Accession No. of homologous cDNA. (multiple entries) |
2.4 Sequencer table
| Data name | Sequencer table |
| Description of data contents | List of result of BLAST search for the amino acid sequence determined by gas-phase protein sequencer. |
| File | rpd_sequencer.zip (23 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Spot ID | ID of the spot. |
| Amino sequence | Amino acid sequence of this spot analysed by protein sequencer. |
| Homologous Protein Accession No. | Accession No. of homologous protein. |
| Homologous Protein definition | Definition of homologous protein. |
| Homologous search identities (%) | Identifies percentage of homologous search. |
2.5 cDNA table
| Data name | cDNA table |
| Description of data contents | Results of homology search to cDNA clones in the KOME. |
| File | rpd_cdna.zip (15 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Spot ID | ID of the spot. |
| Accession NO | Accession No. of homologous cDNA. |
| Clone name | Clone name of homologous cDNA. |
| Score | Score |
| Coverage | Coverage |
2.6 Image files
| Data name | Image files |
| Description of data contents | Gel images and associated image files. |
| File | rpd_gel_image.zip (38.5 MB) |
2.7 Protocol
| Data name | Protocol |
| Description of data contents | Protocols for various methods of proteomics. |
| File | rpd_protocol_jp.zip (Japanese version) (535 KB) rpd_protocol_en.zip (English version) (329 KB) |
3. License
Last updated : 2016/02/02
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "Rice Proteome Database © Setsuko Komatsu (National Institute of Crop Science, National Agriculture and Food Research Organization) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
2-1-18 Kannondai Tsukuba, Ibaraki 305-8634, Japan
National Institute of Crop Science, National Agriculture and Food Research Organization
Setsuko Komatsu
E-mail: skomatsu[at]affrc[dot]go[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2016/02/02 | Rice Proteome Database English archive site is opened. |
| 2003/01/07 | Rice Proteome Database (http://gene64.dna.affrc.go.jp/RPD/) is opened. |
5. Literature
Komatsu S.Rice proteome database: a step toward functional analysis of the rice genome.
Plant Mol Biol. 2005 Sep;59(1):179-90.
PMID: 16217611
Komatsu S, Konishi H, Shen S, Yang G.
Rice proteomics: a step toward functional analysis of the rice genome.
Mol Cell Proteomics. 2003 Jan;2(1):2-10.
PMID: 12601077
Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K.
Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D388-92.
PMID: 14681440
Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S.
Proteomics of the rice cell: systematic identification of the protein populations in subcellular compartments.
Mol Genet Genomics. 2004 Jun;271(5):566-76. Epub 2004 Apr 7.
PMID: 15069638
Tanaka N, Konishi H, Khan MM, Komatsu S.
Proteome analysis of rice tissues by two-dimensional electrophoresis: an approach to the investigation of gibberellin regulated proteins.
Mol Genet Genomics. 2004 Jan;270(6):485-96. Epub 2003 Nov 21.
PMID: 14634867
Komatsu S, Yano H.
Update and challenges on proteomics in rice.
Proteomics. 2006 Jul;6(14):4057-68.
PMID: 16786487
6. Contact address
When you have any question about "RPD", contact the following:2-1-18 Kannondai Tsukuba, Ibaraki 305-8634, Japan
National Institute of Crop Science, National Agriculture and Food Research Organization
Setsuko Komatsu
E-mail: skomatsu[at]affrc[dot]go[dot]jp