ASEB: A Web Server for KAT-specific Acetylation Site Prediction



predict.pngPredict based on sequences


Note: Predict(S) is suitable to find the substrate sites on known substrate proteins.

Method: Predict with Swiss-Prot accession number or protein sequence:

Predefine:
CBP/p300     GCN5/PCAF     TIP60/MYST1/2/3/4     HDAC1/HDAC2/HDAC3     SIRT1
Swiss-Prot accession number (recommended) or protein name:

Sequences:



Validation on known human acetylation sites:

The ASEB method was validated by running the leave-one-out method and estimating the background P-value distribution. Each known acetylated peptide (peptide: the lysine site and its surrounding amino acids) was tested by using the other known acetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected were also tested by using all known acetylated peptides as the predefined peptide set.

Known Sensitivity Background Specificity
Total peptides 341 1000
Significant peptides (P-values ≤ 1e-4) 31 9.1% 13 98.7%
Significant peptides (P-values ≤ 1e-3) 51 15.0% 24 97.6%
Significant peptides (P-values ≤ 1e-2) 79 23.2% 52 94.8%
Significant peptides (P-values ≤ 1e-1) 139 40.8% 141 85.9%

Validation on known acetylation sites from other species (independent data set):

The ASEB method was also validated on the known acetylation sites from other species (such as yeast and mouse). download.png
Each known acetylated site was tested by using all known human acetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected from other species were also tested by using all known human acetylated peptides as the predefined peptide set.

Known (Sensitivity) Backgrounda (Specificity) Backgroundb (Specificity)
Total peptides 42 1000 1000
Significant peptides (P-values ≤ 1e-4) 12 (28.6%) 13 (98.7%) 19 (98.1%)
Significant peptides (P-values ≤ 1e-3) 13 (31.0%) 24 (97.6%) 30 (97.0%)
Significant peptides (P-values ≤ 1e-2) 17 (40.5%) 52 (94.8%) 56 (94.4%)
Significant peptides (P-values ≤ 1e-1) 24 (57.1%) 141 (85.9%) 142 (85.8%)

aBackground peptides that were randomly selected from human proteins, the same set as in the first table.
bBackground peptides that were randomly selected from other species.
Note that, this background test set might still contain unreported acetylation sites. The specificity estimated with this test set is therefore very possibly under-estimated.

Validation on known human acetylation sites:

The ASEB method was validated by running the leave-one-out method and estimating the background P-value distribution. Each known acetylated peptide (peptide: the lysine site and its surrounding amino acids) was tested by using the other known acetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected were also tested by using all known acetylated peptides as the predefined peptide set.

Known Sensitivity Background Specificity
Total peptides 112 1000
Significant peptides (P-values ≤ 1e-4) 14 12.5% 1 99.9%
Significant peptides (P-values ≤ 1e-3) 21 18.8% 3 99.7%
Significant peptides (P-values ≤ 1e-2) 25 22.3% 11 98.9%
Significant peptides (P-values ≤ 1e-1) 42 37.5% 68 93.2%

Validation on known acetylation sites from other species (independent data set):

The ASEB method was also validated on the known acetylation sites from other species (such as yeast and mouse). download.png
Each known acetylated site was tested by using all known human acetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected from other species were also tested by using all known human acetylated peptides as the predefined peptide set.

Known (Sentivity) Backgrounda (Specificity) Backgroundb (Specificity)
Total peptides 30 1000 1000
Significant peptides (P-values ≤ 1e-4) 3 (10.0%) 1 (99.9%) 4 (99.6%)
Significant peptides (P-values ≤ 1e-3) 5 (16.7%) 3 (99.7%) 10 (99.0%)
Significant peptides (P-values ≤ 1e-2) 9 (30.0%) 11 (98.9%) 22 (97.8%)
Significant peptides (P-values ≤ 1e-1) 17 (56.7%) 68 (93.2%) 91 (90.9%)

aBackground peptides that were randomly selected from human proteins, the same set as in the first table.
bBackground peptides that were randomly selected from other species.
Note that, this background test set might still contain unreported acetylation sites. The specificity estimated with this test set is therefore very possibly under-estimated.

Validation on known human deacetylation sites:

The dASEB-C1 method was validated by running the leave-one-out method and estimating the background P-value distribution. Each known deacetylated peptide (peptide: lysine site and its surrounding amino acids) was tested by using the other known deacetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected were also tested by using all known deacetylated peptides as the predefined peptide set.

Known Sensitivity Background Specificity
Total peptides 42 1000
Significant peptides (P-values ≤ 1e-4) 2 4.8% 5 99.5%
Significant peptides (P-values ≤ 1e-3) 4 9.5% 17 98.3%
Significant peptides (P-values ≤ 1e-2) 11 26.2% 45 95.5%
Significant peptides (P-values ≤ 1e-1) 21 50.0% 152 84.8%

Validation on known human deacetylation sites:

The dASEB-SIRT1 method was validated by running the leave-one-out method and estimating the background P-value distribution. Each known deacetylated peptide (peptide: lysine site and its surrounding amino acids) was tested by using the other known deacetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected were also tested by using all known deacetylated peptides as the predefined peptide set.

Known Sensitivity Background Specificity
Total peptides 129 1000
Significant peptides (P-values ≤ 1e-4) 4 3.1% 2 99.8%
Significant peptides (P-values ≤ 1e-3) 9 7.0% 6 99.4%
Significant peptides (P-values ≤ 1e-2) 23 17.8% 18 98.2%
Significant peptides (P-values ≤ 1e-1) 54 41.8% 112 88.8%

Validation on known human acetylation sites:

The ASEB method was validated by running the leave-one-out method and estimating the background P-value distribution. Each known acetylated peptide (peptide: lysine site and its surrounding amino acids) was tested by using the other known acetylated peptides as the predefined peptide set. A total of 1000 background peptides that were randomly selected were also tested by using all known acetylated peptides as the predefined peptide set.

Known Sensitivity Background Specificity
Total peptides 35 1000
Significant peptides (P-values ≤ 1e-4) 0 0.0% 0 100.0%
Significant peptides (P-values ≤ 1e-3) 0 0.0% 1 99.9%
Significant peptides (P-values ≤ 1e-2) 4 11.4% 3 99.7%
Significant peptides (P-values ≤ 1e-1) 8 22.9% 20 98.0%