Saccharomyces Protein-protein Interaction Database

Data contents

Materials

Cross references to other interaction datasets
References

Materials

Table 1. Materials for the integrated data
Data	Version	File Name
Gene Ontology	Mar-06		go_200603-termdb-data

SGD gene annotation	31-Mar-06		gene_association.sgd
SGD feature	27-May-06		SGD_features.tab
SGD dbrefs	27-May-06		dbxref.tab
SGD orf translation sequence	13-May-06		orf_trans_all.fasta

NCBI yeast genome	6-Feb-06		*.gbk

DIP	2-Apr-06		Scere20060402.mif

BIND	21-May-05		20050521.ints.txt 20050521.refs.txt

MIPS evidence scheme	25-Feb-05		evidencecat.scheme
MIPS complex scheme	23-Mar-05		complexcat.scheme
MIPS binary interactions	18-Jan-05		PPI_180105.tab
MIPS complex	20-Jun-05		complexcat_data_20062005

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GSP dataset

METHOD

Data filtering criteria
The following GO terms were filtered including all the descendant terms of them:
(i) in BP ontology, 'biological process unknown' (GO:0000004; including 1482 annotations);
(ii) in CC ontology, 'cellular component unknown' (GO:0008372; including 879 annotations), 'extracellular matrix' (GO:0031012), 'extracellular region' (GO:0005576; including 22 annotations), 'synapse' (GO:0045202) and 'virion' (GO:0019012).

Table 2. Distributions of GO terms and the respective yeast protein annotations
Number of	Filtering	CC	BP	CC+BP	Total
GO Terms	Before	1687	10 458	0	12 145
GO Terms	After	1609	10 457	0	12 066

Terms with assignments	Before	367	1146	0	1513
Terms with assignments	After	365	1145	0	1510

Annotated proteins	Before	5892	5893	5892	5893
Annotated proteins	After	5007	4411	4183	5235

Annotated protein pairs	Before	17 354 886	17 360 778	17 354 886	17 360 778
Annotated protein pairs	After	12 532 521	9 726 255	8 746 653	13 512 123

Associations	Before	8736	10 038	0	18 774
Associations	After	7838	8548	0	16 386

Seven known protein-protein interaction datasets
Please refer to the paper (Wu et al. 2006) for details.

Table 3. Numbers of proteins and interactions of the seven known interaction datasets
Number of	Level	Gavin	Ho	Ito	Uetz	MIPS Complexes	MIPS Interactions	de Lichtenberg	Total
Proteins	original	1363	1570	3244	988	1223	1246	299	4768
	CC	1328	1448	2377	806	1175	1194	279	3904
	BP	1256	1338	2052	701	1169	1193	267	3485
	CC+BP	1236	1289	1848	662	1165	1171	258	3310

Interactions	original	3225	3603	4426	932	10 955	1828	711	22 885
	CC	3163	3395	3057	727	10 898	1715	676	20 914
	BP	3066	3143	2736	637	10 808	1715	663	20 069
	CC+BP	3027	3054	2376	592	10 765	1690	643	19 493

Relative Specificity Similarity (RSS) of two proteins annotated in a GO
Please refer to the paper (Wu et al. 2006) for details.

Statistical significance of protein pairs falling in various levels of RSS values
Please refer to the paper (Wu et al. 2006) for details.

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RESULTS

Distribution of all pairs of annotated proteins according to their RSS values

Figure 1. Distributions of the annotated protein pairs with various RSS values in the CC (A) and BP (B) ontologies.

Figure 2. Statistical significance of the quality scoring system in the CC (A) and BP (B) ontologies.

Based on the distribution analysis of Z-scores for CC and BP ontologies, the 11 categories of RSSCC could roughly be divided into three groups with high confidence (H; 0.8 < RSSCC <= 1), medium confidence (M; 0.5 < RSSCC <= 0.8) and low confidence (L; 0 <= RSSCC <= 0.5). Like RSSCC, RSSBP can also be split into three groups, with high confidence (H; 0.8 < RSSBP <= 1), medium confidence (M; 0.4 < RSSBP <= 0.8) and low confidence (L; 0 <= RSSBP <= 0.4). The nine data segments (DSs) contains 4183 proteins and 8 746 653 protein pairs.

Figure 3. Nine data segments (DSs) with different confidences related to CC and BP ontologies (A) and the selection of positives and negatives, as well as GSPs and GSNs (B).

Gold standard positive and negative protein interaction datasets

Our high quality dataset, the ' valid experimental interactions (VEIs)', was composed of MIPS complexes, MIPS small-scale physical interactions, and the integrated interactions by de Lichtenberg et al. (de Lichtenberg et al. 2005). There are 12 062 interactions among 1807 proteins in VEIs (Figure 4).

Figure 4. Distribution of interactions in three existing high-quality datasets: MIPS Complexes (in drab olive), MIPS Interactions (in blue), and de Lichtenberg (in saffron yellow).

Figure 5. Distribution of the numbers of valid experimental interactions (VEIs) covered by each of the nine DSs (A), and statistical significance of VEIs in nine DSs using Z-score analysis (B).

Assessment of four known genome-scale experimental datasets

The assessment result is in agreement with the previous studies (Edwards et al. 2002; von Mering et al. 2002).

Figure 6. The sizes of four different genome-scale datasets and the rates of interactions covered by positive and negative datasets (A), as well as gold standard datasets (B).

Yeast protein-protein interaction network

The yeast protein-protein interaction network reconstructed from GSPs comprises 92 257 interactions encompassing 3600 proteins. The whole network consists of 23 connected component (Table 3);

Table 3. Numbers of proteins and interactions of 23
connected components

Connected
component ID

Number of proteins
(dynamic)

Number of
interactions

1

3527 (302)

92 084

2

20

130

3

4

6

4

4 (1)

6

5

3

3

6

3 (1)

3

7

3

3

8

3

3

9

4

3

10

3

3

11

2

1

12

2

1

13

2

1

14

2 (1)

1

15

2

1

16

2

1

17

2

1

18

2

1

19

2

1

20

2 (1)

1

21

2

1

22

2

1

23

2

1

Total

3600 (306)

92 257

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Cross references to other interaction datasets

SPIDer provides general links to connect predicted protein-protein interactions with four other related datasets derived from three databases, namely, DIP, BIND and MIPS. Both DIP and BIND are important databases that contain protein-protein interaction information. MIPS provides all annotated and genome-scale protein interactions, and also compiles data on protein complexes which are converted to binary interactions using the matrix model. The releases of these datasets are shown in Materials.
As a result, there are 15 296 interactions in GSPs which have at least one connection to the four datasets, out of which 2951, 1431, 1135 and 14 452 interactions in our database have cross references to DIP, BIND, MIPS binary interactions and MIPS complexes, respectively.

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References

de Lichtenberg, U., Jensen, L.J., Brunak, S. and Bork, P. (2005) Dynamic complex formation during the yeast cell cycle. Science, 307, 724-727. [ PubMed ]
Edwards, A.M., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J. and Gerstein, M. (2002) Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet, 18, 529-536. [ PubMed ]
von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403. [ PubMed ]
Wu, X., Zhu, L., Guo, J., Zhang, D.Y. and Lin, K. (2006) Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res, 34, 2137-2150. [ PubMed ]

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