title: Genome-wide analysis of immune system genes by expressed sequence Tag profiling.
abstract: Profiling studies of mRNA and microRNA, particularly microarray-based studies, have been extensively used to create compendia of genes that are preferentially expressed in the immune system. In some instances, functional studies have been subsequently pursued. Recent efforts such as the Encyclopedia of DNA Elements have demonstrated the benefit of coupling RNA sequencing analysis with information from expressed sequence tags (ESTs) for transcriptomic analysis. However, the full characterization and identification of transcripts that function as modulators of human immune responses remains incomplete. In this study, we demonstrate that an integrated analysis of human ESTs provides a robust platform to identify the immune transcriptome. Beyond recovering a reference set of immune-enriched genes and providing large-scale cross-validation of previous microarray studies, we discovered hundreds of novel genes preferentially expressed in the immune system, including noncoding RNAs. As a result, we have established the Immunogene database, representing an integrated EST road map of gene expression in human immune cells, which can be used to further investigate the function of coding and noncoding genes in the immune system. Using this approach, we have uncovered a unique metabolic gene signature of human macrophages and identified PRDM15 as a novel overexpressed gene in human lymphomas. Thus, we demonstrate the utility of EST profiling as a basis for further deconstruction of physiologic and pathologic immune processes.
authors.affiliation: Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Cosmas C
authors.initials: CC
authors.lastname: Giallourakis
authors.forename: Yair
authors.initials: Y
authors.lastname: Benita
authors.forename: Benoit
authors.initials: B
authors.lastname: Molinie
authors.forename: Zhifang
authors.initials: Z
authors.lastname: Cao
authors.forename: Orion
authors.initials: O
authors.lastname: Despo
authors.forename: Henry E
authors.initials: HE
authors.lastname: Pratt
authors.forename: Lawrence R
authors.initials: LR
authors.lastname: Zukerberg
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
authors.forename: John D
authors.initials: JD
authors.lastname: Rioux
authors.forename: Ramnik J
authors.initials: RJ
authors.lastname: Xavier
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004268:DNA-Binding Proteins / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D007107:Immune System / Q000378:metabolism*; D007154:Immune System Diseases / Q000235:genetics; D016393:Lymphoma, B-Cell / Q000235:genetics; D051379:Mice; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D004268:DNA-Binding Proteins; C502397:PRDM15 protein, human; D062085:RNA, Long Noncoding; D014157:Transcription Factors