Skip to main content

Table 2 Top scoring GO classes from one of the positive datasets

From: Generation of Gene Ontology benchmark datasets with various types of positive signal

    Correlation with signal classes
cl. Num. log10(p) Class names 13 12 9 5 6
1 5.152 metal ion transporter activity -0.005 -0.0078 -0.0068 -0.0067 0.9068
2 4.8916 carboxylic acid transport 0.0266 -0.0088 -0.0076 0.8561 0.0165
3 4.7933 organic acid transport 0.0262 -0.0089 -0.0077 0.8475 0.0162
4 4.6381 tRNA ligase activity -0.0048 -0.0075 0.9863 -0.0064 -0.0064
5 4.6381 amino acid transport -0.0048 -0.0075 -0.0065 1 -0.0064
6 4.6381 di-, tri-valent inorganic cation transporter activity -0.0048 -0.0075 -0.0065 -0.0064 1
7 4.6381 ligase activity, forming carbon-oxygen bonds -0.0048 -0.0075 0.9863 -0.0064 -0.0064
8 4.6381 ligase activity, formingaminoacyl-tRNA and relatedcompounds -0.0048 -0.0075 0.9863 -0.0064 -0.0064
9 4.5219 RNA ligase activity -0.0048 -0.0076 1 -0.0065 -0.0065
10 4.2093 carboxylic acid transporter activity 0.0269 -0.0087 -0.0075 0.7439 0.0168
11 4.1976 ligase activity, forming phosphoric ester bonds -0.005 -0.0079 0.9615 -0.0068 -0.0068
12 4.1196 bud tip -0.0056 1 -0.0076 -0.0075 -0.0075
13 4.0201 response to inorganic substance 1 -0.0056 -0.0048 -0.0048 -0.0048
14 3.9477 organic acid transporter activity 0.0258 -0.0089 -0.0078 0.7214 0.0159
15 3.8469 transition metal ion transporter activity -0.0042 -0.0066 -0.0057 -0.0057 0.8813
16 3.7791 iron ion transporter activity -0.0025 -0.0039 -0.0034 -0.0034 0.5258
17 3.6126 tRNA aminoacylation for protein translation -0.0044 -0.0068 0.8395 -0.0059 -0.0059
18 3.6126 amino acid activation -0.0044 -0.0068 0.8395 -0.0059 -0.0059
19 3.6126 tRNA aminoacylation -0.0044 -0.0068 0.8395 -0.0059 -0.0059
20 3.5079 ion transporter activity -0.0092 -0.0144 -0.0125 -0.0123 0.5218
21 3.4751 amine transport -0.0055 0.0121 -0.0075 0.8651 -0.0074
22 3.3985 amino acid transporter activity -0.0045 -0.0071 -0.0061 0.9128 -0.0061
23 3.2561 cation transporter activity -0.0085 -0.0134 -0.0116 -0.0115 0.5605
24 3.246 di-, tri-valent inorganic cation transport 0.0258 -0.0089 -0.0078 0.0159 0.7685
25 3.1866 transporter activity -0.0055 -0.0192 -0.023 0.2493 0.2833
26 3.1644 transition metal ion transport 0.0291 -0.0082 -0.0071 0.0186 0.6841
27 3.0334 basic amino acid transporter activity -0.0022 -0.0035 -0.0031 0.4702 -0.003
28 2.9412 siderophore-iron transporter activity -0.0016 -0.0025 -0.0022 -0.0021 0.3324
29 2.9412 siderophore transporter activity -0.0016 -0.0025 -0.0022 -0.0021 0.3324
30 2.9035 metal ion transport 0.0241 -0.0094 -0.0081 0.0144 0.733
  1. Table shows 30 most over-represented GO classes from the dataset, ordered with the log10(p-values). Dataset was generated with artificial signal embedded to five classes, shown with bold font in the class list. Table shows also correlation of each reported class with these signal classes. The clear strongest correlation is shown here with bold font. Signal classes are marked in columns using their ranking in the result list. Notice the varying number of strong correlations that different signal classes have.