Table 2.
Gene Ontology annotation for 90e set sequences.
| GO | Molecular Function | Count | Freq% | GO | Biological Process | Count | Freq% | GO | Cellular Component | Count | Freq% |
| GO:0000166 | nucleotide binding | 54,823 | --- | --- | --- | --- | --- | GO:0043229 | intracellular organelle | 60,817 | --- |
| --- | unannotated | 9,709 | --- | --- | unannotated | 62,834 | --- | --- | unannotated | 11,131 | --- |
| GO:0016787 | hydrolase activity | 5,197 | 35.669 | GO:0043170 | macromolecule metabolic process | 5,793 | 35.610 | GO:0043234 | protein complex | 2,918 | 40.788 |
| GO:0016740 | transferase activity | 2,030 | 13.933 | GO:0022607 | cellular component assembly | 2,182 | 13.413 | GO:0044424 | intracellular part | 2,314 | 32.346 |
| GO:0043167 | ion binding | 1,323 | 9.080 | GO:0006810 | transport | 1,213 | 7.456 | GO:0031982 | vesicle | 819 | 11.448 |
| GO:0003735 | structural constituent of ribosome | 874 | 5.999 | GO:0006950 | response to stress | 1,070 | 6.577 | GO:0044425 | membrane part | 469 | 6.556 |
| GO:0005488 | binding | 761 | 5.223 | GO:0050789 | regulation of biological process | 1,012 | 6.221 | GO:0016020 | membrane | 210 | 2.935 |
| GO:0016491 | oxidoreductase activity | 703 | 4.825 | GO:0006807 | nitrogen compound metabolic process | 722 | 4.438 | GO:0005622 | intracellular | 111 | 1.552 |
| GO:0022857 | transmembrane transporter activity | 678 | 4.653 | GO:0048869 | cellular developmental process | 655 | 4.026 | GO:0044446 | intracellular organelle part | 91 | 1.272 |
| GO:0030235 | nitric-oxide synthase regulator activity | 597 | 4.097 | GO:0065009 | regulation of molecular function | 622 | 3.823 | GO:0005576 | extracellular region | 63 | 0.881 |
| GO:0043176 | amine binding | 580 | 3.981 | GO:0009056 | catabolic process | 507 | 3.117 | GO:0045211 | postsynaptic membrane | 21 | 0.294 |
| GO:0005515 | protein binding | 532 | 3.651 | GO:0044419 | interspecies interaction between organisms | 280 | 1.721 | GO:0044420 | extracellular matrix part | 19 | 0.266 |
| GO:0003676 | nucleic acid binding | 401 | 2.752 | GO:0055114 | oxidation reduction | 236 | 1.451 | GO:0043233 | organelle lumen | 18 | 0.252 |
| GO:0005215 | transporter activity | 387 | 2.656 | GO:0065008 | regulation of biological quality | 206 | 1.266 | GO:0031012 | extracellular matrix | 16 | 0.224 |
| GO:0016829 | lyase activity | 71 | 0.487 | GO:0048856 | anatomical structure development | 193 | 1.186 | GO:0042597 | periplasmic space | 15 | 0.210 |
| GO:0016853 | isomerase activity | 55 | 0.377 | GO:0051649 | establishment of localization in cell | 183 | 1.125 | GO:0000267 | cell fraction | 15 | 0.210 |
| GO:0048037 | cofactor binding | 52 | 0.357 | GO:0044237 | cellular metabolic process | 182 | 1.119 | GO:0044462 | external encapsulating structure part | 11 | 0.154 |
| GO:0016874 | ligase activity | 49 | 0.336 | GO:0023060 | signal transmission | 150 | 0.922 | GO:0031975 | envelope | 8 | 0.112 |
| GO:0004871 | signal transducer activity | 45 | 0.309 | GO:0048870 | cell motility | 141 | 0.867 | GO:0005615 | extracellular space | 7 | 0.098 |
| GO:0003824 | catalytic activity | 32 | 0.220 | GO:0008152 | metabolic process | 139 | 0.854 | GO:0009986 | cell surface | 6 | 0.084 |
| GO:0060589 | nucleoside-triphosphatase regulator activity | 32 | 0.220 | GO:0023033 | signaling pathway | 107 | 0.658 | GO:0043204 | perikaryon | 5 | 0.070 |
| GO:0042277 | peptide binding | 28 | 0.192 | GO:0044238 | primary metabolic process | 83 | 0.510 | GO:0030427 | site of polarized growth | 4 | 0.056 |
| GO:0022892 | substrate-specific transporter activity | 22 | 0.151 | GO:0042221 | response to chemical stimulus | 69 | 0.424 | GO:0042995 | cell projection | 3 | 0.042 |
| GO:0019208 | phosphatase regulator activity | 12 | 0.082 | GO:0006996 | organelle organization | 47 | 0.289 | GO:0030312 | external encapsulating structure | 2 | 0.028 |
| GO:0003712 | transcription cofactor activity | 12 | 0.082 | GO:0007017 | microtubule-based process | 42 | 0.258 | GO:0031594 | neuromuscular junction | 2 | 0.028 |
| GO:0019207 | kinase regulator activity | 11 | 0.075 | GO:0044281 | small molecule metabolic process | 39 | 0.240 | GO:0045177 | apical part of cell | 2 | 0.028 |
| GO:0008289 | lipid binding | 9 | 0.062 | GO:0051301 | cell division | 37 | 0.227 | GO:0019028 | viral capsid | 1 | 0.014 |
| GO:0005201 | extracellular matrix structural constituent | 8 | 0.055 | GO:0022613 | ribonucleoprotein complex biogenesis | 35 | 0.215 | GO:0031252 | cell leading edge | 1 | 0.014 |
| GO:0050840 | extracellular matrix binding | 6 | 0.041 | GO:0019637 | organophosphate metabolic process | 34 | 0.209 | GO:0044217 | other organism part | 1 | 0.014 |
| GO:0061134 | peptidase regulator activity | 6 | 0.041 | GO:0045184 | establishment of protein localization | 34 | 0.209 | GO:0044297 | cell body | 1 | 0.014 |
| GO:0030246 | carbohydrate binding | 6 | 0.041 | GO:0009628 | response to abiotic stimulus | 23 | 0.141 | GO:0044463 | cell projection part | 1 | 0.014 |
| GO:0016248 | channel inhibitor activity | 5 | 0.034 | GO:0019748 | secondary metabolic process | 21 | 0.129 | TOTAL | 7,154 | ||
| GO:0003702 | RNA polymerase II transcription factor activity | 5 | 0.034 | GO:0009058 | biosynthetic process | 21 | 0.129 | ||||
| GO:0005198 | structural molecule activity | 4 | 0.027 | GO:0007155 | cell adhesion | 18 | 0.111 | ||||
| GO:0016986 | transcription initiation factor activity | 4 | 0.027 | GO:0061024 | membrane organization | 16 | 0.098 | ||||
| GO:0042165 | neurotransmitter binding | 4 | 0.027 | GO:0007275 | multicellular organismal development | 16 | 0.098 | ||||
| GO:0003682 | chromatin binding | 3 | 0.021 | GO:0016192 | vesicle-mediated transport | 12 | 0.074 | ||||
| GO:0008430 | selenium binding | 3 | 0.021 | GO:0043062 | extracellular structure organization | 10 | 0.061 | ||||
| GO:0030234 | enzyme regulator activity | 2 | 0.014 | GO:0034330 | cell junction organization | 9 | 0.055 | ||||
| GO:0030528 | transcription regulator activity | 2 | 0.014 | GO:0048609 | reproductive process in a multicellular organism | 9 | 0.055 | ||||
| GO:0009055 | electron carrier activity | 2 | 0.014 | GO:0007154 | cell communication | 8 | 0.049 | ||||
| GO:0017056 | structural constituent of nuclear pore | 2 | 0.014 | GO:0003008 | system process | 7 | 0.043 | ||||
| GO:0017080 | sodium channel regulator activity | 2 | 0.014 | GO:0016049 | cell growth | 7 | 0.043 | ||||
| GO:0001871 | pattern binding | 2 | 0.014 | GO:0016458 | gene silencing | 6 | 0.037 | ||||
| GO:0019239 | deaminase activity | 2 | 0.014 | GO:0008219 | cell death | 5 | 0.031 | ||||
| GO:0043021 | ribonucleoprotein binding | 2 | 0.014 | GO:0033036 | macromolecule localization | 4 | 0.025 | ||||
| GO:0008538 | proteasome activator activity | 2 | 0.014 | GO:0048610 | reproductive cellular process | 4 | 0.025 | ||||
| GO:0030337 | DNA polymerase processivity factor activity | 1 | 0.007 | GO:0051236 | establishment of RNA localization | 4 | 0.025 | ||||
| GO:0031406 | carboxylic acid binding | 1 | 0.007 | GO:0071684 | organism emergence from protective structure | 4 | 0.025 | ||||
| GO:0042562 | hormone binding | 1 | 0.007 | GO:0006955 | immune response | 4 | 0.025 | ||||
| GO:0046906 | tetrapyrrole binding | 1 | 0.007 | GO:0007049 | cell cycle | 4 | 0.025 | ||||
| GO:0051540 | metal cluster binding | 1 | 0.007 | GO:0009405 | pathogenesis | 4 | 0.025 | ||||
| TOTAL | 14,570 | GO:0009607 | response to biotic stimulus | 4 | 0.025 | ||||||
| GO:0009791 | post-embryonic development | 4 | 0.025 | ||||||||
| GO:0048646 | anatomical structure formation involved in morphogenesis | 4 | 0.025 | ||||||||
| GO:0009790 | embryonic development | 3 | 0.018 | ||||||||
| GO:0015976 | carbon utilization | 2 | 0.012 | ||||||||
| GO:0032506 | cytokinetic process | 2 | 0.012 | ||||||||
| GO:0045103 | intermediate filament-based process | 2 | 0.012 | ||||||||
| GO:0070882 | cellular cell wall organization or biogenesis | 2 | 0.012 | ||||||||
| GO:0006413 | translational initiation | 2 | 0.012 | ||||||||
| GO:0009566 | fertilization | 2 | 0.012 | ||||||||
| GO:0001906 | cell killing | 1 | 0.006 | ||||||||
| GO:0043473 | pigmentation | 1 | 0.006 | ||||||||
| GO:0009987 | cellular process | 1 | 0.006 | ||||||||
| GO:0022402 | cell cycle process | 1 | 0.006 | ||||||||
| GO:0022411 | cellular component disassembly | 1 | 0.006 | ||||||||
| GO:0022415 | viral reproductive process | 1 | 0.006 | ||||||||
| GO:0023061 | signal release | 1 | 0.006 | ||||||||
| GO:0030030 | cell projection organization | 1 | 0.006 | ||||||||
| GO:0051606 | detection of stimulus | 1 | 0.006 | ||||||||
| GO:0000746 | conjugation | 1 | 0.006 | ||||||||
| GO:0007163 | establishment or maintenance of cell polarity | 1 | 0.006 | ||||||||
| GO:0009653 | anatomical structure morphogenesis | 1 | 0.006 | ||||||||
| TOTAL | 16,268 | ||||||||||
The most probable GO code in the three ontology categories--molecular function, biological process and cellular component-- for each sequence in the 90e data set was selected. For simplicity, only level one and two codes are shown here in order.