GO Cardiovascular: Introduction to GO Annotation for the Cardiovascular Initiative
A Rough Guide to GO Annotation
In simple terms, a GO annotation is the manual or electronic association of a GO term representing a biological process, cellular component, or molecular function term with a gene product. The evidence for the association is captured by recording the reference, and the nature of the evidence is classified using a code from the GO evidence code set. Every GO annotation created by the GO Consortium follows strict annotation guidelines; see the GO annotation guide for more information.
The process of annotation (the association of GO terms to gene products) can be carried out either manually or automatically. The large-scale assignment of gene products to GO terms using automatic methods is a fast and efficient way of creating a large set of annotations. However, in order for these associations to be correct many of these electronic GO annotations use high level (i.e. rather general) GO terms and often only provide the most minimal overview of the associated gene products functions. Details on the electronic methods applied can be found in Camon et al., 2004 and the GO References page. Manual, comprehensive GO annotations created by assessing experimental evidence from the latest published literature produces far more reliable and detailed GO annotation sets. Manual annotation is a slow, expensive activity, however, and annotation groups need to carefully prioritize their annotation target sets.
The cardiovascular GO annotation initiative will focus on manual annotation of human genes known, or thought, to be involved in cardiovascular processes. Since November 2007, two annotators skilled in GO curation have begun to manually and comprehensively annotate the experimental literature associated with the list of cardiovascular relevant genes. During the course of this project, 1500 well-known genes relevant to the cardiovascular system will be comprehensively annotated, with the close involvement of many cardiovascular groups.
An example of the improved information that can be supplied by carrying out GO annotation can be seen in the example below:
| GO term | Evidence code | Reference |
|---|---|---|
Biological Process (2 terms) |
||
| GO:0006366 : transcription from RNA polymerase II promoter | TAS | PMID:10823886 [external website] |
| GO:0007179 : transforming growth factor beta receptor signaling pathway | TAS | PMID:8774881 [external website] |
Molecular Function (2 terms) |
||
| GO:0003700 : transcription factor activity | TAS | PMID:10823886 [external website] |
| GO:0005515 : protein binding | IPI | PMID:14612439 [external website] |
Cellular Component (1 term) |
||
| GO:0005622 : intracellular | IC | PMID:14612439 [external website] |
| GO term | Evidence code | Reference |
|---|---|---|
Biological Process (14 terms) |
||
| GO:0006366 : transcription from RNA polymerase II promoter | TAS | PMID:10823886 [external website] |
| GO:0000122 : negative regulation of transcription from RNA polymerase II promoter | IDA | PMID:8774881 [external website] |
| GO:0001666 : response to hypoxia | IMP | PMID:12411310 [external website] |
| GO:0006917 : induction of apoptosis | IMP | PMID:15334054 [external website] |
| GO:0006919 : caspase activation | IMP | PMID:15107418 [external website] |
| GO:0007050 : cell cycle arrest | IMP | PMID:14555988 [external website] |
| GO:0007183 : SMAD protein complex assembly | IDA | PMID:10823886 [external website] |
| GO:0017015 : regulation of transforming growth factor beta receptor signaling pathway | IMP | PMID:8774881 [external website] |
| GO:0019049 : evasion of host defenses by virus | IDA | PMID:15334054 [external website] |
| GO:0030308 : negative regulation of cell growth | IDA | PMID:8774881 [external website] |
| GO:0032909 : regulation of transforming growth factor-beta2 production | IMP | PMID:12411310 [external website] |
| GO:0042993 : positive regulation of transcription factor import into nucleus | IDA | PMID:15799969 [external website] |
| GO:0045930 : negative regulation of mitotic cell cycle | IMP | PMID:14555988 [external website] |
| GO:0045944 : positive regulation of transcription from RNA polymerase II promoter | IDA | PMID:8774881 [external website] |
Molecular Function (6 terms) |
||
| GO:0003700 : transcription factor activity | TAS | PMID:10823886 [external website] |
| GO:0005515 : protein binding | IPI | PMID:14612439 [external website] |
| GO:0015460 : transport accessory protein activity | IDA | PMID:15799969 [external website] |
| GO:0042803 : protein homodimerization activity | IPI | PMID:8774881 [external website] |
| GO:0043565 : sequence-specific DNA binding | IDA | PMID:10823886 [external website] |
| GO:0046332 : SMAD binding | IPI | PMID:8774881 [external website] |
Cellular Component (4 terms) |
||
| GO:0005622 : intracellular | IC | PMID:14612439 [external website] |
| GO:0005634 : nucleus | IDA | PMID:12446380 [external website] |
| GO:0005737 : cytoplasm | IDA | PMID:12446380 [external website] |
| GO:0043235 : receptor complex | IMP | PMID:8774881 [external website] |
Recommended reading
The following article provides a general introduction to GO for biologists:
Get ready to GO! A biologist's guide to the Gene Ontology.
Brief Bioinform. 2005 ; 6: 298-304. (PubMed abstract [external website])
The following article provides a general introduction to the GOA database at EBI and explains electronic and manual annotation techniques:
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
Nucleic Acids Res. 2004 ; 32: D262-D266. (PubMed abstract [external website]; full text [external website])
