Gene Ontology
AmiGO
Two entries were found when searching for BRCA1 in Homo sapiens in AmiGO.
First entry:
Cellular components: cytoplasm, nucleus, and condensed chromosome
Molecular function: damaged DNA binding and zinc ion binding
Biological process: DNA replication, DNA repair, chordate embryonic development, dosage compensation, by inactivation of the X chromosome, cell cycle checkpoint, and centrosome cycle
Second entry:
Cellular components: nucleoplasm, BRCA1-BARD1 complex, and gamma-tubulin ring complex
Molecular function: enzyme binding, identical protein binding, zinc ion binding, transcription coactivator activity, tubulin binding, and androgen receptor binding
Biological process: DNA damage response, signal transduction resulting in induction of apoptosis, chromosome segregation, regulation of transcription from RNA polymerase II promoter, regulation of cell proliferation, positive regulation of transcription, DNA-dependent, negative regulation of transcription, negative regulation of cell cycle, androgen receptor signaling pathway, negative regulation of fatty-acid biosynthetic pathway, positive regulation of protein ubiquitination, double-strand break repair via homologous recombination, DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator, negative regulation of centriole replication, positive regulation of DNA repair, postreplication repair, regulation of transcription from RNA polymerase III promoter, and response to estrogen stimulus
Both entries contained links to protein database entries, as well as crystal structures of the protein.
These results are available in a graphical view, shown below. Click on picture to link out to interactive website.
From AmiGO, 2009. BRCA1-BARD1 Complex Graphical View. Retrieved from http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?session_id=2277amigo1238274058&term=GO:0031436&format=png.
GOA
The only GO entry found with Gene Ontology Annotation (GOA) was the BRCA1-BARD1 complex.
GO id: GO:0031436
Below is an image of an ancestor chart provided by this website. The GO id's on the original website are linked to the GO entries for each term. [1]
Figure 1. Ancestor tree of GO terms associated with BRCA1-BARD1 complex from the GOA website. Click on figure to link out to the GOA website for interactive links (Select the Ancestor Table tab). "P" indicates "part of" and "I" indicates "is a."
From GOA, 2009. BRCA1 Ancestor Table. Retrieved from http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031436.
Possibly easier to interpret visually than the table in Figure 1 is the ancestor chart from the GOA website. Unfortunately the image was to large for me to capture for this website.
GO ALL
GO ALL allows searching of a gene, GO ID, or term in a quick search. Annotations for many species were returned when BRCA1 was searched. When the Homo sapiens BRCA1 protein was selected, 40 GO terms were returned in an easy-to-read table. Clicking on each GO term category gave an explanation of the group and a list of proteins implicated in the process.
Analysis
Most of the GO terms found were very predictable based on the function of BRCA1. These were the terms that were related to being in the nucleus, being involved in DNA repair, and containing a RING finger domain. Terms that I did not know were related to BRCA1 were androgen receptor binding, roles in protein ubiquitination, and transcriptional regulation. All of these unexpected terms were found using AmiGO and GO ALL. GOA gave mostly cell component terms and was less detailed.
All three of the databases I used were very helpful for finding GO terms by searching for a gene of interest. I would like to note that may other databases are available for using the GO terms themselves as search terms or using large datasets to derive GO associations, but for the purpose of this website, I chose to omit these. AmiGO, GOA, and GO ALL were all very user-friendly, but each provided a different way of presenting the data in a way that may suit different individuals. For example, GOA was much more visual than AmiGO and GO ALL, and GO ALL presented descriptions of the category instead of a code.
AmiGO and GO ALL provided more detailed lists of GO terms, most of which overlapped between the two databases. GOA had fewer GO terms in the table, but covered the most relevant categories for the gene. Selecting databases based on level of detail desired and the method of presentation of results provides user-specificity.
[1] Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. (2009) The GOA database in 2009--an
integrated Gene Ontology Annotation resource. Nucleic Acids Research 2009 37: D396-D403.
doi:10.1093/nar/gkn803
Site created by Jessica D. Kueck
Genetics 677 Assignment, Spring 2009
University of Wisconsin-Madison
