Gene Ontology Newsletter

Issue No. 4

February 2007

Gene of the Quarter: MSH2

MSH2 graph

MSH2 is a member of a highly conserved family of proteins involved in DNA mismatch repair that includes E. coli MutS and S. cerevisiae Msh2p. Mutations in human MSH2 result in hereditary nonpolyposis colorectal cancer (HNPCC) and several sporadic cancers. Linking the human MSH2 gene to HNPCC was facilitated by prior characterization of E. coli MutS and S. cerevisiae Msh2p (Fishel R, Lescoe MK, Rao MR, Copeland NG, Jenkins NA, Garber J, Kane M, Kolodner R. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. [PMID:8252616]).

In order to summarize the knowledge in the published literature for MSH2, 125 GO annotations based on experimental evidence were made for the human MSH2 and its predicted orthologs. For organisms where there is no experimental data about the protein, GO annotations were made based on sequence similarity to these experimentally characterized proteins. The annotations are consistent with the known role of MSH2 in DNA repair but the variety of terms used in the annotations illustrates the level of experimental knowledge in each species and may point to subtle functional differences. View the full version of the graphical representation of the MSH2 annotations shown on the right or download these (and other) annotations for an organism from the annotation downloads on the GO website.

About "Gene of the Quarter": In 2006, the GO consortium initiated the reference genome project to provide complete GO annotations for orthologs of human disease genes in a set of 12 model organisms. A gene will be selected from this project to highlight how studies done in one model organism can help decipher a gene's role in another organism and in causing a disease, how the experimental evidence has been annotated using GO, and how to further access these annotations. Please contact the GO Consortium with comments, additional annotations, or suggestions for disease-related genes to annotate.

RSC Publishing is GO!

Beginning in February 2007, all Royal Society of Chemistry (RSC) Publishing electronic journal articles will be enhanced to highlight compounds and scientific concepts. These highlighted words are hyperlinks to allow readers to download structures of chemical compounds, link to topic-specific online databases, and find related articles. Terms from the Gene Ontology and the Sequence Ontology, as well as several other classification systems, will be used to highlight the scientific concepts in the articles. Compounds and ontology terms will be published as RSS feeds, enabling automated discovery of relevant research. More information is available from Project Prospect.

GO Now is_a complete

In January, Biological Process became the final ontology to be made "is_a complete", meaning each term in the hierarchy has at least one is_a relationship path to the top node (see Newsletter Issue 1). This change also resulted in various improvements to the ontology such as the introduction of new top-level terms to distinguish single cell, multi-cellular and multi-organism processes.

New Evidence Code: Inferred from Genomic Context (IGC)

A new evidence code, "Inferred from Genomic Context" (IGC), has been added to the GO set for use when an annotation attached to a gene product is derived using information about other gene products in a genome. These additional genes can be neighbors, as in operons and syntenic regions, or spread throughout the genome. An example of an IGC-based annotation is metabolic pathway reconstruction, in which an annotator looks for a required set of gene products to assert that a pathway occurs in a particular organism. The presence of the entire required set of genes is evidence that each gene in the set can be annotated to the biological process in question. See the evidence code documentation for additional information on IGC. Please contact the Gene Ontology Consortium if you have any questions.

New Genomes Annotated with GO

TIGR has released GO annotations for three genomes from tick-borne bacteria: Neorickettsia sennetsu, Ehrlichia chaffeensis and Anaplasma phagocytophilum. These and other annotations may be downloaded from the GO website.

TIGR GO Annotation Courses

The following annotation courses are being offered at TIGR in 2007:

There will not be a GOC manual annotation camp this year.

Upcoming Meetings

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Please contact the Gene Ontology Consortium with any comments or suggestions. Frequently asked questions will appear as tutorials or tips in upcoming newsletters.