title: CEM-designer: design of custom expression microarrays in the post-ENCODE Era.
abstract: Microarrays are widely used in gene expression studies, and custom expression microarrays are popular to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes uncovered recently make custom expression microarray design a non-trivial task. Pervasive transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that requires well-considered probe design strategies and is largely neglected in existing approaches. We developed the web server CEM-Designer that facilitates microarray platform independent design of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection and generation of a set of unique target sequences from different sources and (ii) the selection of a set of sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to third party software to ensure that probes meet provider-specific constraints. CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de.
authors.affiliation: Bioinformatics Group, Department for Computer Science, University of Leipzig, Leipzig, Germany; RNomics Group, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Arnold
authors.affiliation: Bioinformatics Group, Department for Computer Science, University of Leipzig, Leipzig, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Externbrink
authors.affiliation: Young Investigators Group, Bioinformatics and Transcriptomics, Department Proteomics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Bioinformatics Group, Department for Computer Science, University of Leipzig, Leipzig, Germany; RNomics Group, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany. Electronic address: joerg.hackermueller@ufz.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.affiliation: Young Investigators Group, Bioinformatics and Transcriptomics, Department Proteomics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Bioinformatics Group, Department for Computer Science, University of Leipzig, Leipzig, Germany; RNomics Group, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany. Electronic address: kristin.reiche@ufz.de.
authors.forename: Kristin
authors.initials: K
authors.lastname: Reiche
mesh_terms: D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D022661:RNA, Untranslated / Q000235:genetics
chemical_list: D022661:RNA, Untranslated
keywords: Custom expression microarray; Microarray design; Non-coding RNA; Pervasive transcription; Transcriptomics