title: InnateDB: facilitating systems-level analyses of the mammalian innate immune response.
abstract: Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner.
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. dlynn@sfu.ca
authors.forename: David J
authors.initials: DJ
authors.lastname: Lynn
authors.forename: Geoffrey L
authors.initials: GL
authors.lastname: Winsor
authors.forename: Calvin
authors.initials: C
authors.lastname: Chan
authors.forename: Nicolas
authors.initials: N
authors.lastname: Richard
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Laird
authors.forename: Aaron
authors.initials: A
authors.lastname: Barsky
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Gardy
authors.forename: Fiona M
authors.initials: FM
authors.lastname: Roche
authors.forename: Timothy H W
authors.initials: TH
authors.lastname: Chan
authors.forename: Naisha
authors.initials: N
authors.lastname: Shah
authors.forename: Raymond
authors.initials: R
authors.lastname: Lo
authors.forename: Misbah
authors.initials: M
authors.lastname: Naseer
authors.forename: Jaimmie
authors.initials: J
authors.lastname: Que
authors.forename: Melissa
authors.initials: M
authors.lastname: Yau
authors.forename: Michael
authors.initials: M
authors.lastname: Acab
authors.forename: Dan
authors.initials: D
authors.lastname: Tulpan
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Whiteside
authors.forename: Avinash
authors.initials: A
authors.lastname: Chikatamarla
authors.forename: Bernadette
authors.initials: B
authors.lastname: Mah
authors.forename: Tamara
authors.initials: T
authors.lastname: Munzner
authors.forename: Karsten
authors.initials: K
authors.lastname: Hokamp
authors.forename: Robert E W
authors.initials: RE
authors.lastname: Hancock
authors.forename: Fiona S L
authors.initials: FS
authors.lastname: Brinkman