Table 3.
Comparison between DIAN and MGI Ontological Assignments
| Results from the comparative approach are shown. A number of intrinsic problems were identified from this approach, such that type I and type II variances described here are for comparative purposes only and cannot be interpreted strictly as type I and II errors. |
| Table 3A. Comparing Assignments Made to the Cellular Role Ontology |
| Concept | DIAN node number | Highest level matching GO modes | Present in | Variation | Sensitivity | Selectivity | |||
| DIAN and GO | DIAN only | GO only | Type I | Type II | |||||
| Chromosome structure | 1.1 | GO:0007001;GO:0006323 | 7 | 4 | 4 | 0.267 | 0.267 | 0.636 | 0.636 |
| Transcription factors | 1.4 | GO:0003700 | 59 | 54 | 38 | 0.358 | 0.252 | 0.608 | 0.522 |
| DNA duplication | 3.2 | GO:0006260;GO:0003964 | 10 | 2 | 2 | 0.143 | 0.143 | 0.833 | 0.833 |
| Cell-cell adhesion | 5.2 | GO:0007155 | 35 | 15 | 14 | 0.234 | 0.219 | 0.714 | 0.700 |
| Transcription factors | 9.1.1.1 | GO:0008135 | 1 | 0 | 1 | 0.000 | 0.500 | 0.500 | 1.000 |
| Microtubule | 6.2 | GO:0007017 | 9 | 0 | 2 | 0.000 | 0.182 | 0.818 | 1.000 |
| DNA repair | 8.1 | GO:0006281 | 14 | 2 | 9 | 0.080 | 0.360 | 0.609 | 0.875 |
| Programmed cell death | 8.2 | GO:0006915 | 14 | 7 | 23 | 0.159 | 0.523 | 0.378 | 0.667 |
| Channel and transporter | 4.6 | GO:0006810;GO:0005216 | 47 | 8 | 27 | 0.098 | 0.329 | 0.635 | 0.855 |
| Amino acid metabolism | 9.2 | GO:0006519 | 4 | 1 | 7 | 0.083 | 0.407 | 0.476 | 0.625 |
| Stress response | 8.4 | GO:0006950 | 5 | 6 | 55 | 0.091 | 0.833 | 0.083 | 0.455 |
| Nucleotide metabolism | 9.4 | GO:0006140:0006205 | 0 | 2 | 7 | 0.222 | 0.778 | 0.000 | 0.000 |
| GO:0006143 | |||||||||
| Cofactor metabolism | 9.5 | GO:0006731 | 4 | 0 | 3 | 0.000 | 0.429 | 0.571 | 1.000 |
| Total DIAN and GO: 229 | |||||||||
| TotalDIAN only: 113 | |||||||||
| Total GO only: 214 | |||||||||
| Total: 556 | |||||||||
| Average type I: 0.203 | |||||||||
| Average type II: 0.385 | |||||||||
| Sensitivity: 0.517 | |||||||||
| Selectivity: 0.670 | |||||||||
| DIAN assignments made to a group of well-characterized, nonredundant mouse sequences were compared to assignments made by the MGI to the GO Process and Function ontologies. GO modes corresponding to DIAN nodes are listed, along with the abbreviated essential concept from theDIAN Role ontology. For brevity, only the highest level GO nodes are listed. The number of sequences whose assignment is shared to both sets of ontologies is indicated (DIAN and GO), as well as the number of sequence assignments which differed (DIANonly, GO only). These numbers are used to calculate Type I and II variation using the following equations: Type I variation =DIANonly/(DIAN and GO +DIAN only + GO only); Type II variation = GO only/(DIAN and GO +DIAN only + GO only); Sensitivity =DIAN and GO/(DIAN and GO + GO only); Selectivity =DIAN and GO/(DIAN and GO +DIAN only). Sensitivity is defined as the ability of the DIAN algorithm to make what are believed to be all possible correct assignments. Selectivity is defined as the ability of the DIANalgorithm to not make what is believed to be an incorrect assignment. |
| Table 3B. Comparing Assignments Made to the Protein Function Ontology |
| Concept | DIAN node number | Highest level matching GO modes | Present in | Variation | Sensitivity | Selectivity | |||
| DIAN and GO | DIAN only | GO only | Type I | Type II | |||||
| Hormones and active peptides | 10 | GO:0005179;GO:0005103 | 7 | 3 | 8 | 0.167 | 0.444 | 0.467 | 0.700 |
| GO:0005104;GO:0005105 | |||||||||
| GO:0005106;GO:0005109 | |||||||||
| GO:0005110;GO:0005111 | |||||||||
| GO:0005112;GO:0005113 | |||||||||
| GO:0005114;GO:0005115 | |||||||||
| GO:0005116;GO:0005117 | |||||||||
| GO:0005118;GO:0005119 | |||||||||
| GO:0005120;GO:0005121 | |||||||||
| GO:0005122;GO:0005123 | |||||||||
| GO:0005124;GO:0005177 | |||||||||
| GO:0005178;GO:0005186 | |||||||||
| Inhibitors | 12 | GO:0004857;GO:0008189 | 12 | 3 | 9 | 0.125 | 0.375 | 0.571 | 0.800 |
| GO:0005074;GO:0005092 | |||||||||
| GO:0008200;GO:0005517 | |||||||||
| DNA or RNA associated proteins | 3 | GO:0003676;GO:0003735 | 255 | 21 | 26 | 0.070 | 0.086 | 0.907 | 0.924 |
| GO:0004748;GO:0003910 | |||||||||
| GO:0003911;GO:0004518 | |||||||||
| GO:0003899;GO:0008534 | |||||||||
| GO:0008263;GO:0003907 | |||||||||
| GO:0003905;GO:0003906 | |||||||||
| GO:0003904 | |||||||||
| GO:0004844;GO:0003908 | |||||||||
| Protein secretion and chaperones | 13 | GO:0003754;GO:0008565 | 11 | 3 | 2 | 0.188 | 0.125 | 0.846 | 0.786 |
| GO:0006605 | |||||||||
| Electron transport proteins | 5 | GO:0005489 | 0 | 7 | 6 | 0.538 | 0.462 | 0.000 | 0.000 |
| Other tranport proteins | 6 | GO:0005215 | 62 | 17 | 19 | 0.173 | 0.194 | 0.765 | 0.785 |
| Structural proteins | 7 | GO:0005198 | 31 | 23 | 40 | 0.245 | 0.426 | 0.437 | 0.574 |
| Receptors | 8 | GO:0004872 | 67 | 43 | 15 | 0.344 | 0.120 | 0.817 | 0.609 |
| Cytokines and growth factors | 9 | GO:0008083;GO:0005125 | 35 | 19 | 10 | 0.297 | 0.156 | 0.778 | 0.648 |
| GO:0008009 | |||||||||
| TotalDIAN and GO: 480 | |||||||||
| TotalDIAN only: 139 | |||||||||
| Total GO only: 135 | |||||||||
| Total: 754 | |||||||||
| Average type I: 0.184 | |||||||||
| Average type II: 0.179 | |||||||||
| Sensitivity: 0.780 | |||||||||
| Selectivity: 0.775 | |||||||||
-
A group of well-characterized, nonredundant mouse sequences were assigned to the Protein Function ontology by theDIAN domain-based mapping algorithm. These assignments were compared to assignments made to the GO Process and Function ontology by the MGI.
