Details zur Publikation

Referenztyp Zeitschriften
DOI / URL Link
Titel (primär) CEM-Designer: design of custom expression microarrays in the post-ENCODE era
Autor Arnold, C.; Externbrink, F.; Hackermüller, J.; Reiche, K.;
Journal / Serie Journal of Biotechnology
Erscheinungsjahr 2014
Department PROTEOM;
Band/Volume 189
Sprache englisch;
POF III (gesamt) T42;
Keywords Transcriptomics; Pervasive transcription; Non-coding RNA; Custom expression microarray; Microarray design
UFZ Querschnittsthemen 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.
ID 15362
dauerhafte UFZ-Verlinkung 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