About This Database

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

Data description

Data name

DOI

10.18908/lsdba.nbdc00742-001

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;<a href="http://www.yeastgenome.org/" rel="external">http://www.yeastgenome.org/</a>, August 15, 2009). The number of data is 841. The data are given in a CSV format text file.

Data file

File name :

core_updated.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/yeast_y2h/LATEST/core_updated.zip

File size :

77KB

Simple search URL

http://togodb.biosciencedbc.jp/togodb/view/yipd_core_updated#en

Data acquisition method

Yeast two-hybrid method. (Fields, S. & Song, O. K. (1989) Nature (London) 340, 245-246.)

Data analysis method

As the indicator of reliability of the interactions obtained by the experiment, the literature information described about the yeast proteins and their interactions are required. Several sources including YPD (Yeast Proteome Database, Costanzo, M. C., Hogan, J. D., Cusick, M. E., Davis, B. P., Fancher, A. M., Hodges, P. E., Kondu, P., Lengieza, C., Lew-Smith, J. E., Lingner, C., et al. (2000) Nucleic Acids Res. 28, 73-76.) are used for literature collection.

Number of data entries

841 interactions

Data detail

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)(*1).
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:
CuraGen(0 or 1)	Investigation by CuraGen (0 or 1), obtained from Uetz et al.(*2)
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(*3).
Expression similarity (BRITE)	Expression data obtained from KEGG BRITE(*4). (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.