title: A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.
abstract: The analysis of patient blood transcriptional profiles offers a means to investigate the immunological mechanisms relevant to human diseases on a genome-wide scale. In addition, such studies provide a basis for the discovery of clinically relevant biomarker signatures. We designed a strategy for microarray analysis that is based on the identification of transcriptional modules formed by genes coordinately expressed in multiple disease data sets. Mapping changes in gene expression at the module level generated disease-specific transcriptional fingerprints that provide a stable framework for the visualization and functional interpretation of microarray data. These transcriptional modules were used as a basis for the selection of biomarkers and the development of a multivariate transcriptional indicator of disease progression in patients with systemic lupus erythematosus. Thus, this work describes the implementation and application of a methodology designed to support systems-scale analysis of the human immune system in translational research settings.
authors.affiliation: Baylor NIAID Cooperative Center for Translational Research on Human Immunology and Biodefense, Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX 75204, USA. damienc@baylorhealth.edu
authors.forename: Damien
authors.initials: D
authors.lastname: Chaussabel
authors.forename: Charles
authors.initials: C
authors.lastname: Quinn
authors.forename: Jing
authors.initials: J
authors.lastname: Shen
authors.forename: Pinakeen
authors.initials: P
authors.lastname: Patel
authors.forename: Casey
authors.initials: C
authors.lastname: Glaser
authors.forename: Nicole
authors.initials: N
authors.lastname: Baldwin
authors.forename: Dorothee
authors.initials: D
authors.lastname: Stichweh
authors.forename: Derek
authors.initials: D
authors.lastname: Blankenship
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Indira
authors.initials: I
authors.lastname: Munagala
authors.forename: Lynda
authors.initials: L
authors.lastname: Bennett
authors.forename: Florence
authors.initials: F
authors.lastname: Allantaz
authors.forename: Asuncion
authors.initials: A
authors.lastname: Mejias
authors.forename: Monica
authors.initials: M
authors.lastname: Ardura
authors.forename: Ellen
authors.initials: E
authors.lastname: Kaizer
authors.forename: Laurence
authors.initials: L
authors.lastname: Monnet
authors.forename: Windy
authors.initials: W
authors.lastname: Allman
authors.forename: Henry
authors.initials: H
authors.lastname: Randall
authors.forename: Diane
authors.initials: D
authors.lastname: Johnson
authors.forename: Aimee
authors.initials: A
authors.lastname: Lanier
authors.forename: Marilynn
authors.initials: M
authors.lastname: Punaro
authors.forename: Knut M
authors.initials: KM
authors.lastname: Wittkowski
authors.forename: Perrin
authors.initials: P
authors.lastname: White
authors.forename: Joseph
authors.initials: J
authors.lastname: Fay
authors.forename: Goran
authors.initials: G
authors.lastname: Klintmalm
authors.forename: Octavio
authors.initials: O
authors.lastname: Ramilo
authors.forename: A Karolina
authors.initials: AK
authors.lastname: Palucka
authors.forename: Jacques
authors.initials: J
authors.lastname: Banchereau
authors.forename: Virginia
authors.initials: V
authors.lastname: Pascual
mesh_terms: D000293:Adolescent; D002648:Child; D019295:Computational Biology / Q000379:methods; D018450:Disease Progression; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006801:Humans; D008180:Lupus Erythematosus, Systemic / Q000097:blood* / Q000235:genetics*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*