Once a list of differentially expressed genes has been generated, the next task is determining the biological significance of those genes. By combining the identification of broad biological themes with the ability to focus on a particular gene, it is possible to rapidly characterize the biology involved in a particular experiment, and to identify particular genes of interest from a very long list of potential targets.

Gene Annotation Sources

•  GenBank:Sequence information for particular clones and probes.
•  UniGene: Sets of sequences that represent unique genes, and information for those genes.
•  LocusLink: Curated sequence and descriptive information about genes.
•  Gene Ontology: Controlled vocabularies for the description of molecular function, biological process and cellular component of gene products.
•  KEGG: Information about both regulatory and metabolic pathways for genes.
•  OMIM: A catalog of human genes and genetic disorders.
•  HomoloGene: A gene homology tool that compares nucleotide sequences between pairs of organisms.

Utilizing these resources of is the best way to determine the biological significance of a gene of interest.

Single genes

•  Gene summaries: Taken together, the information provided by annotation sources for a particular gene is a useful summary of knowledge about that gene.

These summaries can be used to identify targets for further study, or to prioritize the genes on the list, based, for example, on their involvement in a biological process of interest.

Gene List

•  Ontology report: A summary of ontology information for a gene list, including how many genes in a list have a particular ontology, and how many genes on the array have that ontology.
•  Pathway report: Similar information for pathways assigned to genes in a list.

  By examining ontology reports or pathway reports for the gene list as a whole, broad biological themes may be identified.