IGC: Inferred from Genomic Context

Updated November 9, 2007

  • operon structure
  • syntenic regions
  • pathway analysis
  • genome scale analysis of processes

This evidence code can be used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation. Genomic context includes, but is not limited to, such things as identity of the genes neighboring the gene product in question (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis.

IGC may be used in situations where part of the evidence for the function of a protein is that it is present in a putative operon for which the other members of the operon have strong sequence or literature based evidence for function. The presence of the gene in an operon specific for a particular function, pathway, complex, etc. is itself a form of evidence. It is encouraged that when using this code with operon structure that the id numbers for the genes in the operon be put in the with/from field.

The IGC evidence code can also be used to annotate gene products encoded by genes within a region of conserved synteny. For instance, sequence similarity alone may be too low to make an inference but orthology can often be predicted based on the position of a gene within a region of synteny and this used to strengthen the assertion. In these cases the with/from field should be used to store the identity of the positional ortholog.

In the area of process annotations, in order for us to assert that a gene product is involved in a particular process in the cell, that process itself must be happening in that cell. The only way to know if a process is happening is to determine if all of the elements required for that process are present. This is often accomplished by looking to see if there are genes in the genome which can complete every step in the process in question. The same holds true for subunits of protein complexes. This often entails examining many different gene products and many different evidence types found all around the genome of an organism to reach a particular conclusion.

When the method used to make annotations using the IGC code is performed internally by the annotating group and is not published, a short description of the method should be written and added to the GO Consortium's collection of GO references, where it will be given a GO_REF ID which can be used to cite the reference in gene association files.

Usage of the With/From Column for IGC

We recommend making an entry in the with/from column when using this evidence code. In cases where operon structure or synteny are the compelling evidence, include identifier(s) for the neighboring genes in the with/from column. In casees where metabolic reconstruction is the compelling evidence, and there is an identifier for the pathway or system, that should be entered in the with/from column. When multiple entries are placed in the with/from field, they are separated by pipes.

Note that there has been some discrepancy between groups as to the use of the with/from column; please see the Note on Usage of the With/from Column for more details.

...

2.

DB Object ID

3.

DB Object Symbol

4.

Qualifier

5.

GO ID

6.

DB:Reference

7.

Evidence Code

8.

With/From

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... TIGR_CMR:gene_B_ID gene B   GO:0009231 GO_REF:0000025 IGC operon_geneA_ID|operon_geneC_ID (from operon in annotated organism) ...
... TIGR_CMR:gene_A_ID gene A   GO:0009102 PMID:15347579 IGC TIGR_GenProp:GenProp0036 ...