1. Novel genes identified by manual annotation and microarray expression analysis in the pancreas
- Author
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Alexey Katokhin, Alexandre Shilov, Marina Gubina, Athanasios Arsenlis, Nadezhda Vorobjeva, Nikolay A. Kolchanov, Peter White, Eugenij Elisafenko, Olga Belova, Polina Perelman, Vladimir Trifonoff, Vera Bogdanova, Deborah F. Pinney, Klaus H. Kaestner, John Brestelli, Christian J. Stoeckert, Lilia Nizolenko, Mikhail Puzakov, Joan M. Mazzarelli, and Regina K. Gorski
- Subjects
Signal peptide ,DNA, Complementary ,Microarray ,Transcription, Genetic ,Annotation ,MicroRNA Gene ,Biology ,Clones ,03 medical and health sciences ,Islets of Langerhans ,Mice ,0302 clinical medicine ,Mice, Inbred NOD ,Complementary DNA ,Gene expression ,Genetics ,Animals ,Cloning, Molecular ,Gene ,Pancreas ,030304 developmental biology ,0303 health sciences ,Genome ,Microarray analysis techniques ,Gene Expression Profiling ,Islet cells ,Computational Biology ,Proteins ,Transcript ,Microarray Analysis ,Gene expression profiling ,Diabetes Mellitus, Type 1 ,030217 neurology & neurosurgery ,cDNA array - Abstract
The mouse PancChip, a microarray developed for studying endocrine pancreatic development and diabetes, represents over 13,000 cDNAs. After computationally assigning the cDNAs on the array to known genes, manual curation of the remaining sequences identified 211 novel transcripts. In microarray experiments, we found that 196 of these transcripts were expressed in total pancreas and/or pancreatic islets. Of 50 randomly selected clones from these 196 transcripts, 92% were confirmed as expressed by qRT-PCR. We evaluated the coding potential of the novel transcripts and found that 74% of the clones had low coding potential. Since the transcripts may be partial mRNAs, we examined their translated proteins for transmembrane or signal peptide domains and found that about 40 proteins had one of these predicted domains. Interestingly, when we investigated the novel transcripts for their overlap with noncoding microRNAs, we found that 1 of the novel transcripts overlapped a known microRNA gene.
- Published
- 2006