Yeast Interacting Proteins Database

2010/02/15

WebSite: Yeast Interacting Proteins Database
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/yeast_y2h

Information on interactions and related information obtained by the comprehensive yeast two-hybrid analysis of budding yeast proteins.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Core Data of Yeast Interacting Proteins Database (Annotation Updated Version)
  3. Full Data of Yeast Interacting Proteins Database (Annotation Updated Version)
  4. Core Data of Yeast Interacting Proteins Database (Original Version)
  5. Full Data of Yeast Interacting Proteins Database (Original Version)
Return to Top

2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Yeast Interacting Proteins Database" data.
File README_e.html(English)
Return to Top

2.2 Core Data of Yeast Interacting Proteins Database (Annotation Updated Version)

Data name Core Data of Yeast Interacting Proteins Database (Annotation Updated Version)
Description of data contents

Highly reproducible interaction data in the Yeast Interacting Proteins Database with the "IST hit" (to be described in the table below) of 3 or more. Annotation (gene name and description) is updated by the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/, August 15, 2009). The number of data is 841. The data are given in a CSV format text file.

File core_updated.zip (77KB)
Data items are the following:
Data item Description
Bait ORF The ORF name of Bait, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/).
Bait gene name The gene name of Bait, and the standard name in the SGD.
Bait description The annotation of Bait, and description in the SGD.
Rows with this bait as bait The number of rows (interactions) having this Bait ORF as the Bait ORF, and the link to the search results (for TogoDB only).
Rows with this bait as prey The number of rows (interactions) having this Bait ORF as the Prey ORF, and the link to the search results (for TogoDB only).
Prey ORF The ORF name of Prey, and the systematic name in the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org).
Prey gene name The gene name of Prey, and the standard name in the SGD.
Prey description The annotation of Prey, and description in the SGD.
Rows with this prey as prey The number of rows (interactions) having this Prey ORF as the Prey ORF, and the link to the search results (for TogoDB only).
Rows with this prey as bait The number of rows (interactions) having this Prey ORF as the Bait ORF, and the link to the search results (for TogoDB only).
Literature on bait(YPD) The number of articles concerning Bait, obtained from YPD (Yeast Proteome Database)(*2).
Literature on prey(YPD) The number of articles concerning Prey, obtained from YPD.
Literature shared by bait and prey The number of articles common to Bait and Prey, as calculated on the basis of the number of articles obtained from the YPD.
Literature sharing score The score concerning co-occurrence of Prey and Bait in the literature, calculated by the calculation formula.
Calculation formula for the score:
Literature sharing score
CuraGen(0 or 1) Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*3)
S. Fields(0 or 1) Investigation by S. Fields (0 or 1), obtained from Uetz et al.
Association(0 or 1,YPD) Association (0 or 1), obtained from the YPD.
Complex (0 or 1,YPD) Formation of complex (0 or 1), obtained from the YPD.
Synthetic lethality(0 or 1,YPD) Synthetic lethality (0 or 1), obtained from the YPD.
Co-induced by(YPD) Factor that induces expression of both genes, obtained from the YPD.
Co-repressed by(YPD) Factor that suppresses expression of both genes, obtained from the YPD.
Not affected by(YPD) Factor that does not affect expression of these genes, obtained from the YPD.
Interologs The number of interactions that exist between the interacting protein and the ortholog of other species, obtained from the Database of Interacting Proteins(*4).
Expression similarity (BRITE) Expression data obtained from KEGG BRITE(*5). (High values only, 0.9 or greater)
Alternative path with 1 intervening protein The number of paths other than this interaction mediated by one intermediate protein, calculated from the full data.
Alternative path with 2 intervening proteins The number of paths other than this interaction mediated by two intermediate proteins, calculated from the full data.
IST hit Number of hits of Interaction Sequence Tags (IST) (The number of detected interactions and the indicator of reproducibility)
IST hit in the opposite bait/prey orientation The IST hit number for a combination in which Bait and Prey are in the reverse direction.

2.3 Full Data of Yeast Interacting Proteins Database (Annotation Updated Version)

Data name Full Data of Yeast Interacting Proteins Database (Annotation Updated Version)
Description of data contents

The entire data in the Yeast Interacting Proteins Database. Annotation (gene name and description) is updated by the SGD (Saccharomyces Genome Database;http://www.yeastgenome.org/, August 15, 2009). The number of data is 4,549. The data are given in a CSV format text file.
File full_updated.zip (372KB)
Each item in data is the same as 2.2 Core Data of Yeast Interacting Proteins Database (Annotation Updated Version).

2.4 Core Data of Yeast Interacting Proteins Database (Original Version)

Data name Core Data of Yeast Interacting Proteins Database (Original Version)
Description of data contents

Highly reproducible interaction data in the Yeast Interacting Proteins Database with the "IST hit" (to be described in the table below) of 3 or more. The gene information (gene name and description) is the data at the time the paper(*1) was published. The number of data is 841. The data are given in a CSV format text file.

File core_original.zip (37KB)
Each item in data is the same as 2.2 Core Data of Yeast Interacting Proteins Database (Annotation Updated Version).

2.5 Full Data of Yeast Interacting Proteins Database (Original Version)

Data name Full Data of Yeast Interacting Proteins Database (Original Version)
Description of data contents

The entire data in the Yeast Interacting Proteins Database. The gene information (gene name and description) is the data at the time the paper(*1) was published. The number of data is 841. The data are given in a CSV format text file.

File full_original.zip (180KB)
Each item in data is the same as 2.2 Core Data of Yeast Interacting Proteins Database (Annotation Updated Version).


*1 A comprehensive two-hybrid analysis to explore the yeast protein interactome.,
Costanzo MC, Hogan JD, Cusick ME, Davis BP, Fancher AM, Hodges PE, Kondu P, Lengieza C, Lew-Smith JE, Lingner C, Roberg-Perez KJ, Tillberg M, Brooks JE, Garrels JI., Nucleic Acids Res. 2000 Jan 1;28(1):73-6.
*2 The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.,
Costanzo MC, Hogan JD, Cusick ME, Davis BP, Fancher AM, Hodges PE, Kondu P, Lengieza C, Lew-Smith JE, Lingner C, Roberg-Perez KJ, Tillberg M, Brooks JE, Garrels JI., Nucleic Acids Res. 2000 Jan 1;28(1):73-6.
*3 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.,
Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM., Nature. 2000 Feb 10;403(6770):623-7.
*4 DIP: the database of interacting proteins.,
Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D., Nucleic Acids Res. 2000 Jan 1;28(1):289-91.
*5 KEGG: kyoto encyclopedia of genes and genomes.,
Kanehisa M, Goto S., Nucleic Acids Res. 2000 Jan 1;28(1):27-30.

Return to Top

3. License

The Standard License specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The Additional License specifies those items that are exceptionally permitted even though they are generally prohibited in the Standard License.

3.1 Standard License

The Standard License for this database is the license specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "Yeast Interacting Proteins Database, Copyright© 2009 Takashi Ito(the University of Tokyo) licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the Standard License, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under this License.

3.2 Additional License

1. You must display this Additional License along with the Standard License when distributing any derivative work based on part of whole of the data from this database.

2. When you conduct research by using this database, and describe the research results in an article or paper, you always need to cite this database, and specify the name and URL of this database in the article or paper.

3.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 Standard License and the above Additional License.

GSFS - CB-06, Transdisciplinary Sciences, The University of Tokyo
5-1-5 Kashiwanoha, Kashiwa-shi, Chiba-ken
277-8561
Tel: +81-4-7136-3989
FAX: +81-4-7136-3979
E-mail : ito[at]bi[dot]s[dot].u-tokyo[dot]ac[dot]jp

3.3 About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

Return to Top

4. Update History

Date Update contents
2010/03/29 Yeast Interacting Proteins Database English archive site is opened.
2000/12/4 Yeast Interacting Proteins Database(http://itolab.cb.k.u-tokyo.ac.jp/Y2H/) is released.
Return to Top

5. Literature

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins.
Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y.
Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1143-7.
PMID: 10655498

A comprehensive two-hybrid analysis to explore the yeast protein interactome.
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y.
Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74. Epub 2001 Mar 13.
PMID: 11283351

6. Contact address

When you have any question about "Yeast Interacting Proteins Database", contact the following:

GSFS - CB-06, Transdisciplinary Sciences, The University of Tokyo
5-1-5 Kashiwanoha, Kashiwa-shi, Chiba-ken
277-8561
Tel: +81-4-7136-3989
FAX: +81-4-7136-3979
E-mail : ito[at]bi[dot]s[dot].u-tokyo[dot]ac[dot]jp

Return to Top