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CEM-Designer: Design of custom expression microarrays in the post-ENCODE Era

: Arnold, Christian; Externbrink, Fabian; Hackermüller, Jörg; Reiche, Kristin


Journal of biotechnology 189 (2014), S.154-156
ISSN: 0168-1656
ISSN: 1389-0352
ISSN: 1873-4863
Fraunhofer IZI ()
transcriptomics; pervasive transcription; non-coding RNA; custom expression microarray; microarray design

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