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Genomics. 2006 Dec;88(6):752-761. doi: 10.1016/j.ygeno.2006.04.005. Epub 2006 May 24.

Novel genes identified by manual annotation and microarray expression analysis in the pancreas.

Author information

1
Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: mazz@pcbi.upenn.edu.
2
Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
3
Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
4
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.

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.

PMID:
16725306
DOI:
10.1016/j.ygeno.2006.04.005
[Indexed for MEDLINE]
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