Table 1.
List of evidence codes used by EcoCyc to tag transcription units (TUs), sorted by the number of polycistronic operons with constituent transcription units that are tagged to the evidence code. Note that the evidence codes are grouped into classes based on the second word in each code: “EXP” = experimental evidence, “COMP” = computational evidence, “IC” = inferred by database curator.
| Evidence code | Description | # of tagged TUs | # of polycistronic operons w/ tagged TUs |
|---|---|---|---|
| EV-COMP-AINF | Automated inference from computational evidence48 | 1447 | 392 |
| EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION | Inferred from experimentally measured transcript lengths | 606 | 161 |
| EV-EXP-IDA-BOUNDARIES-DEFINED | Inferred from sites or genes bounding the transcription unit that have been experimentally identified | 675 | 156 |
| EV-EXP-IEP-COREGULATION | Inferred from the existence of adjacent genes that are transcribed in the same direction and exhibit similar expression patterns under a range of environmental conditions | 226 | 144 |
| EV-EXP-IMP-POLAR-MUTATION | Inferred from experiments demonstrating polar effects | 168 | 97 |
| EV-IC-ADJ-GENES-SAME-BIO-PROCESS | Inferred from the existence of adjacent genes that are transcribed in the same direction and encode for products used in the same biological process | 115 | 71 |
| EV-EXP-IEP | Inferred from expression patterns (e.g. northern blots, microarrays) | 106 | 58 |
| EV-IC | Inferred by curators from relevant information such as other assertions in a database | 70 | 31 |
| EV-COMP-HINF | Human inference from computational evidence48 | 71 | 21 |
| EV-EXP-IDA | Inferred from a direct experimental assay | 4 | 3 |
| EV-AS-NAS | Inferred from a non-traceable author statement without a reference to the publication supporting the assertion | 4 | 3 |
| EV-AS-TAS | Inferred from a traceable author statement that references another publication supporting the assertion, but it is unclear whether the reference describes an experiment that supports the assertion | 4 | 3 |
| EV-COMP-AINF-SINGLE-DIRECTON | Automated inference based on a single-gene directon76, where a single gene is transcribed in the opposite direction from its upstream and downstream genes | 441 | 2 |
| EV-COMP-IBA | Inferred from characterization of an ancestral gene | 1 | 1 |
| EV-AS-HYPO | Inferred from an author hypothesis, without clear experimental evidence supporting the hypothesis | 1 | 1 |
| EV-ND | No biological evidence data available | 1 | 1 |
| EV-EXP-TAS | Inferred from a traceable author statement that references another publication describing an experiment supporting the assertion | 3 | 1 |
| EV-HTP-HEP | Inferred from high-throughput expression pattern | 1 | 1 |
| EV-EXP | Inferred from experiment | 1 | 1 |
| EV-EXP-IMP | Inferred from mutant phenotypes | 10 | 0 |