title: Towards multidimensional genome annotation.
abstract: Our information about the gene content of organisms continues to grow as more genomes are sequenced and gene products are characterized. Sequence-based annotation efforts have led to a list of cellular components, which can be thought of as a one-dimensional annotation. With growing information about component interactions, facilitated by the advancement of various high-throughput technologies, systemic, or two-dimensional, annotations can be generated. Knowledge about the physical arrangement of chromosomes will lead to a three-dimensional spatial annotation of the genome and a fourth dimension of annotation will arise from the study of changes in genome sequences that occur during adaptive evolution. Here we discuss all four levels of genome annotation, with specific emphasis on two-dimensional annotation methods.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, California, 92093, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Reed
authors.forename: Iman
authors.initials: I
authors.lastname: Famili
authors.forename: Ines
authors.initials: I
authors.lastname: Thiele
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
mesh_terms: D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D025941:Protein Interaction Mapping / Q000379:methods* / Q000639:trends
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins