Table 1.
Clustering and CLASSIFI results for data from 3 ligands
| GO ID | g | f | c | n | expt | prob | GO type | GO term | Cluster ID | anti-CD40 | LPS | AIG |
| GO:0005634 | 2490 | 254 | 380 | 64 | 38.76 | 8.71E-06 | CC | Nucleus | 1 | 1 | 1 | 1 |
| GO:0009058 | 2490 | 141 | 180 | 25 | 10.19 | 1.36E-05 | BP | biosynthesis | 2 | 1 | 1 | |
| GO:0008372 | 2490 | 1409 | 1 | 1 | 0.566 | 5.66E-01 | CC | CC unknown | 3 | 1 | -1 | -1 |
| GO:0046072 | 2490 | 2 | 160 | 2 | 0.129 | 4.10E-03 | BP | dTDP metabolism | 4 | 1 | 1 | |
| GO:0009605 | 2490 | 30 | 3 | 2 | 0.036 | 4.18E-04 | BP | response to external stimulus | 5 | 1 | -1 | |
| GO:0016655 | 2490 | 14 | 331 | 11 | 1.861 | 4.94E-08 | MF | oxidoreductase activity, acting on NADH | 6 | 1 | ||
| GO:0005773 | 2490 | 12 | 11 | 4 | 0.053 | 1.00E-07 | CC | Vacuole | 7 | -1 | -1 | 1 |
| GO:0003779 | 2490 | 15 | 277 | 9 | 1.669 | 6.30E-06 | MF | actin binding | 8 | -1 | -1 | -1 |
| GO:0016758 | 2490 | 6 | 245 | 4 | 0.59 | 1.17E-03 | MF | Transferase activity, transferring hexosyl groups | 9 | -1 | -1 | |
| GO:0006417 | 2490 | 2 | 4 | 1 | 0.003 | 3.21E-03 | BP | regulation of protein biosynthesis | 10 | -1 | 1 | |
| GO:0008372 | 2490 | 1409 | 41 | 32 | 23.2 | 3.30E-03 | CC | CC unknown | 11 | -1 | -1 | |
| GO:0008047 | 2490 | 10 | 160 | 3 | 0.643 | 2.23E-02 | MF | enzyme activator activity | 12 | -1 | ||
| GO:0006397 | 2490 | 19 | 56 | 4 | 0.427 | 6.92E-04 | BP | mRNA processing | 13 | 1 | 1 | |
| GO:0005576 | 2490 | 156 | 183 | 33 | 11.47 | 7.28E-09 | CC | extracellular | 14 | 1 | ||
| GO:0046916 | 2490 | 1 | 4 | 1 | 0.002 | 1.61E-03 | BP | transition metal ion homeostasis | 15 | -1 | 1 | |
| GO:0003931 | 2490 | 3 | 38 | 2 | 0.046 | 6.74E-04 | MF | Rho small monomeric GTPase activity | 16 | -1 | -1 | |
| GO:0004032 | 2490 | 3 | 188 | 3 | 0.227 | 4.24E-04 | MF | aldehyde reductase activity | 17 | -1 | ||
| GO:0015672 | 2490 | 10 | 191 | 7 | 0.767 | 1.38E-06 | BP | monovalent inorganic cation transport | 18 | 1 | ||
| GO:0016892 | 2490 | 3 | 50 | 2 | 0.06 | 1.17E-03 | MF | endoribonuclease activity, producing other than | 19 | -1 |
Gene clusters (Cluster ID 1–19) resulting from categorical clustering of processed data from B cells stimulated with anti-CD40, LPS, and AIG. "1" = upregulated, "-1" = downregulated, and blank = no significant change. Following CLASSIFI analysis, the GO term giving rise to the lowest probability in each gene cluster is indicated. GO ID = a unique Gene Ontology identifier assigned to a GO term that corresponds to a defined molecular function (MF), biological process (BP), or cellular component (CC). g = number of probes in the data set, f = number of probes with associated GO ID in the data set, c = number of probes in the gene cluster, n = number of probes with associated GO ID in the gene cluster. Expt = the expected number of occurrences of a given GO ID in a given cluster of size (n) based on a random distribution. Prob = the probability that the GO ID co-cluster pattern has occurred by chance.