 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. |
| 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:
 |
| 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. |
*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.
|
