IC: Inferred by Curator

Updated September 22, 2011 

The IC evidence code is to be used for those cases where an annotation is not supported by any direct evidence, but can be reasonably inferred by a curator from other GO annotations, for which evidence is available.

An example would be when there is evidence (be it direct assay, sequence similarity or even from electronic annotation) that a particular gene product has the function RNA polymerase II transcription factor activity ; GO:0003702. There is no direct evidence showing that this gene product is located in the nucleus, but this would be a perfectly reasonable inference for a curator to make since the curator is annotating a eukaryotic gene product that is associated with a specific nuclear RNA polymerase. This inference will be linked to the annotation to the term RNA polymerase II transcription factor activity ; GO:0003702 in two ways: both annotations will share the same reference; and the annotation inferred by a curator will include one or more with/from statements pointing to the GO term(s) used by the curator for the inference.

In many cases a GO term can be inferred from just one other annotation as described above. Occasionally, there are cases where a curator has to infer the GO term based on evidence from multiple sources of evidence/GO annotations. The 'with/from' field in these annotations will therefore supply >1 GO identifier, obtained from the set of supporting GO annotations assigned to the same gene/gene product identifier which cite publicly-available references. In addition, such IC-annotations will use reference GO_REF:0000036.

Usage of the With/From Column for IC

Note that the with/from field must always be filled in with a GO ID when using this evidence code.

For example, Noel et al., 1998 (PMID:9651335) provides evidence that the protein encoded by the S. cerevisiae UGA3 gene has the function "specific RNA polymerase II transcription factor activity" ; GO:0003704. From this, the curator deduces it is located in the nucleus and thus makes an annotation to the cellular component term "nucleus" ; GO:0005634 with the GO ID for the function term in the with/from for the component annotation.

The second example shown below illustrates the use of IC with GO_REF:0000036. In this case, a curator has inferred an annotation for the CUP9 gene to the GO Term "RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding"; GO:0001133 based on evidence from PMID:9427760 that CUP9 is involved in "RNA polymerase II core promoter proximal region sequence-specific DNA binding" (GO:0000978), as well as evidence from PMID:18708352 that CUP9 is involved in "negative regulation of transcription from RNA polymerase" (GO:0000122). The with/from column supplies the GO IDs derived from these two publications separated by comma symbols (meaning AND) because both of these GO terms are required to support the inferred annotation to GO:0001133. If either of the GO terms could support the inference, they should be separated with a pipe (meaning OR).

...

2.

DB Object ID

3.

DB Object Symbol

4.

Qualifier

5.

GO ID

6.

DB:Reference

7.

Evidence Code

8.

With/From

...
... SGDID:S000002329 UGA3   GO:0003704 PMID:9651335 IPI   ...
... SGDID:S000002329 UGA3   GO:0005634 PMID:9651335 IC GO:0003704 ...

...

2.

DB Object ID

3.

DB Object Symbol

4.

Qualifier

5.

GO ID

6.

DB:Reference

7.

Evidence Code

8.

With/From

...
... SGDID:S000006098 CUP9   GO:0000122 PMID:18708352 IMP   ...
... SGDID:S000006098 CUP9   GO:0000978 PMID:9427760 IDA   ...
... SGDID:S000006098 CUP9   GO:0001133 GO_REF:0000036 IC GO:0000122,GO:0000978 ...

Where;

  • GO:0003704 specific RNA polymerase II transcription factor activity
  • GO:0005634 nucleus
  • GO:0000122 negative regulation of transcription from RNA polymerase II promoter
  • GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
  • GO:0001133 RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding