CEM-designer: design of custom expression microarrays in the post-ENCODE Era

Christian Arnold; Fabian Externbrink; Jörg Hackermüller; Kristin Reiche

doi:10.1016/j.jbiotec.2014.09.012

CEM-designer: design of custom expression microarrays in the post-ENCODE Era

J Biotechnol. 2014 Nov 10:189:154-6. doi: 10.1016/j.jbiotec.2014.09.012. Epub 2014 Sep 28.

Authors

Christian Arnold¹, Fabian Externbrink², Jörg Hackermüller³, Kristin Reiche⁴

Affiliations

¹ 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.
² Bioinformatics Group, Department for Computer Science, University of Leipzig, Leipzig, Germany.
³ 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: [email protected].
⁴ 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: [email protected].

PMID: 25262644
DOI: 10.1016/j.jbiotec.2014.09.012

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.

Keywords: Custom expression microarray; Microarray design; Non-coding RNA; Pervasive transcription; Transcriptomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Oligonucleotide Array Sequence Analysis / methods*
RNA, Untranslated / genetics

Substances

RNA, Untranslated