title: Noncoder: a web interface for exon array-based detection of long non-coding RNAs.
abstract: Due to recent technical developments, a high number of long non-coding RNAs (lncRNAs) have been discovered in mammals. Although it has been shown that lncRNAs are regulated differently among tissues and disease statuses, functions of these transcripts are still unknown in most cases. GeneChip Exon 1.0 ST Arrays (exon arrays) from Affymetrix, Inc. have been used widely to profile genome-wide expression changes and alternative splicing of protein-coding genes. Here, we demonstrate that re-annotation of exon array probes can be used to profile expressions of tens of thousands of lncRNAs. With this annotation, a detailed inspection of lncRNAs and their isoforms is possible. To allow for a general usage to the research community, we developed a user-friendly web interface called 'noncoder'. By uploading CEL files from exon arrays and with a few mouse clicks and parameter settings, exon array data will be normalized and analysed to identify differentially expressed lncRNAs. Noncoder provides the detailed annotation information of lncRNAs and is equipped with unique features to allow for an efficient search for interesting lncRNAs to be studied further. The web interface is available at http://noncoder.mpi-bn.mpg.de.
authors.affiliation: Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany.
authors.forename: Pascal
authors.initials: P
authors.lastname: Gellert
authors.forename: Yuliya
authors.initials: Y
authors.lastname: Ponomareva
authors.forename: Thomas
authors.initials: T
authors.lastname: Braun
authors.forename: Shizuka
authors.initials: S
authors.lastname: Uchida
mesh_terms: D000818:Animals; D005091:Exons; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D062085:RNA, Long Noncoding