title: Principles for the organization of gene-sets.
abstract: A gene-set, an important concept in microarray expression analysis and systems biology, is a collection of genes and/or their products (i.e. proteins) that have some features in common. There are many different ways to construct gene-sets, but a systematic organization of these ways is lacking. Gene-sets are mainly organized ad hoc in current public-domain databases, with group header names often determined by practical reasons (such as the types of technology in obtaining the gene-sets or a balanced number of gene-sets under a header). Here we aim at providing a gene-set organization principle according to the level at which genes are connected: homology, physical map proximity, chemical interaction, biological, and phenotypic-medical levels. We also distinguish two types of connections between genes: actual connection versus sharing of a label. Actual connections denote direct biological interactions, whereas shared label connection denotes shared membership in a group. Some extensions of the framework are also addressed such as overlapping of gene-sets, modules, and the incorporation of other non-protein-coding entities such as microRNAs.
authors.affiliation: The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA. Electronic address: wli@nshs.edu.
authors.forename: Wentian
authors.initials: W
authors.lastname: Li
authors.affiliation: The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Freudenberg
authors.affiliation: The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA.
authors.forename: Michaela
authors.initials: M
authors.lastname: Oswald
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D005838:Genotype; D006801:Humans; D009369:Neoplasms / Q000175:diagnosis / Q000188:drug therapy / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D049490:Systems Biology
keywords: Biological pathways; Co-differential expression; Co-expression; Co-localization; Disease genes; Essential genes; Gene Ontology (GO); Gene families; Gene-sets; Housekeeping genes; Modules; Operon; Protein complex; Protein domains; Protein–protein interaction; Tissue-specific genes; Transcription factor target