Supplementary Materials
Figure captions
SupFig 1. Positive relationships between average degree and protein expression levels in
different datasets. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C)
in vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset. There are no significant
relationships in D, because this sub-dataset is much smaller. Manual collection subdataset is generally believed to be the most reliable interaction dataset. Therefore, the
positive relationships in B and C confirm that the relationship in A is real.
SupFig 2. Positive relationships between average degree and protein polarity in different
datasets. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C) in vivo
pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 3. Soluble proteins in general have many more interaction partners than
membrane proteins. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C)
in vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 4. Negative relationships between average degree and fraction of random coils in
different datasets. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C)
in vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 5. Negative relationships between average degree and fraction of strands in
different datasets. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C)
in vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 6. Positive relationships between average degree and fraction of helices in
different datasets. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C)
in vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 7. Proteins with at least one functional annotation have many more interaction
partners than those without any functional annotations based on MIPS functional
classification. (A) Whole interaction dataset. (B) Manual collection sub-dataset. (C) in
vivo pull-down sub-dataset. (D) Yeast two-hybrid sub-dataset.
SupFig 8. in vivo pull-down sub-dataset is systematically biased again small proteins.
The number of proteins in the in vivo pull-down sub-dataset in each bin has a good linear
relationship with the average protein length in each bin, which results in the positive
relationship between average degree and protein length in the whole interaction dataset.
80
B
45
Average degree (K)
70
Average degree (K)
50
A
60
50
40
30
20
40
35
30
25
20
15
10
10
5
0
0
0.1
1
10
0.1
100
Expression level (lnE)
120
10
100
Expression Level (LnE)
6
C
D
5
Average degree (K)
100
Average degree (K)
1
80
60
40
20
4
3
2
1
0
0
0.1
1
10
Expression Level (LnE)
100
0.1
1
10
100
Expression Level (LnE)
SupFig 1
45
40
B
10
35
Average degree (K)
Average degree (K)
12
A
30
25
20
15
10
8
6
4
2
5
0
0
7
7.5
8
8.5
9
9.5
10
7
7.5
8
Protein polarity
70
9
9.5
10
9
9.5
10
Protein polarity
6
C
60
D
5
Average degree (K)
Average degree (K)
8.5
50
40
30
20
4
3
2
1
10
0
0
7
7.5
8
8.5
Protein polarity
9
9.5
10
7
7.5
8
8.5
Protein polarity
SupFig 2
35
9
A
Average degree (K)
Average degree (K)
25
20
15
10
B
8
30
5
7
6
5
4
3
2
1
0
0
S
1
2
3
4
5
6
7
8
9
10
11
12
S
≥13
1
2
3
4
5
7
8
9
10
11
12
≥13
Protein solubility
Protein solubility
80
4
C
60
50
40
30
20
D
3.5
Average degree (K)
70
Average degree (K)
6
3
2.5
2
1.5
1
0.5
10
0
0
S
1
2
3
4
5
6
7
8
Protein solubility
9
10
11
12
≥13
S
1
2
3
4
5
6
7
8
9
10
11
12
≥13
Protein solubility
SupFig 3
12
45
40
10
35
Average degree (K)
Average degree (K)
B
A
30
25
20
15
10
8
6
4
2
5
0
0
0.3
0.35
0.4
0.45
0.5
0.55
0.6
0.65
0.7
0.3
0.75
0.35
0.4
0.5
0.55
0.6
0.65
0.7
0.75
Fraction of random coils
Fraction of random coils
70
6
C
60
D
5
Average degree (K)
Average degree (K)
0.45
50
40
30
20
4
3
2
1
10
0
0
0.3
0.35
0.4
0.45
0.5
0.55
0.6
Fraction of random coils
0.65
0.7
0.75
0.3
0.35
0.4
0.45
0.5
0.55
0.6
0.65
0.7
0.75
Fraction of random coils
SupFig 4
45
40
B
10
35
Average degree (K)
Average degree (K)
12
A
30
25
20
15
10
8
6
4
2
5
0
0
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0
0.05
0.1
0.15
Fraction of strands
0.25
0.3
0.35
0.4
0.45
Fraction of strands
70
4.5
C
Average degree (K)
50
40
30
20
10
D
4
60
Average degree (K)
0.2
3.5
3
2.5
2
1.5
1
0.5
0
0
0
0.05
0.1
0.15
0.2
0.25
Fraction of strands
0.3
0.35
0.4
0.45
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
Fraction of strands
SupFig 5
60
18
A
Average degree (K)
50
Average degree (K)
B
16
40
30
20
10
14
12
10
8
6
4
2
0
0
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0
0.1
0.2
Fraction of helices
80
0.4
0.5
0.6
0.7
0.5
0.6
0.7
Fraction of helices
5
C
D
4.5
70
60
Average degree (K)
Average degree (K)
0.3
50
40
30
20
10
4
3.5
3
2.5
2
1.5
1
0.5
0
0
0
0.1
0.2
0.3
0.4
Fraction of helices
0.5
0.6
0.7
0
0.1
0.2
0.3
0.4
Fraction of helices
SupFig 6
40
10
A
Average degree (K)
Average degree (K)
8
30
25
20
15
10
5
7
6
5
4
3
2
1
0
0
Proteins with functional annotations
Proteins without functional
annotations
60
Proteins with functional annotations
Proteins without functional
annotations
4
C
D
3.5
Average degree (K)
50
Average degree (K)
B
9
35
40
30
20
10
3
2.5
2
1.5
1
0.5
0
0
Proteins with functional annotations
Proteins without functional
annotations
Proteins with functional annotations
Proteins without functional
annotations
SupFig 7
400
350
# of protiens
300
250
200
y = 0.1819x + 104.6
R2 = 0.7602
P < 10-4
150
100
50
0
0
500
1000
1500
Protein length (# of amino acids, N)
SupFig 8