Publication Details |
| Reference Category | Journals |
| DOI / URL | link |
| Title (Primary) | CEM-Designer: design of custom expression microarrays in the post-ENCODE era |
| Author | Arnold, C.; Externbrink, F.; Hackermüller, J.; Reiche, K. |
| Journal | Journal of Biotechnology |
| Year | 2014 |
| Department | PROTEOM |
| Volume | 189 |
| Page From | 154 |
| Page To | 156 |
| Language | englisch |
| Keywords | Transcriptomics; Pervasive transcription; Non-coding RNA; Custom expression microarray; Microarray design |
| UFZ wide themes | RU3; |
| 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. |
| Persistent UFZ Identifier | https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=15362 |
| Arnold, C., Externbrink, F., Hackermüller, J., Reiche, K. (2014): CEM-Designer: design of custom expression microarrays in the post-ENCODE era J. Biotechnol. 189 , 154 - 156 |
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