title: Novel genes identified by manual annotation and microarray expression analysis in the pancreas.
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.
authors.affiliation: 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.
authors.forename: Joan M
authors.initials: JM
authors.lastname: Mazzarelli
authors.affiliation: Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: White
authors.affiliation: 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.
authors.forename: Regina
authors.initials: R
authors.lastname: Gorski
authors.affiliation: 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.
authors.forename: John
authors.initials: J
authors.lastname: Brestelli
authors.affiliation: 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.
authors.forename: Deborah F
authors.initials: DF
authors.lastname: Pinney
authors.affiliation: Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Arsenlis
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Katokhin
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Belova
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Vera
authors.initials: V
authors.lastname: Bogdanova
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Eugenij
authors.initials: E
authors.lastname: Elisafenko
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Marina
authors.initials: M
authors.lastname: Gubina
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Lilia
authors.initials: L
authors.lastname: Nizolenko
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Polina
authors.initials: P
authors.lastname: Perelman
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Puzakov
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Shilov
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Trifonoff
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Nadezhda
authors.initials: N
authors.lastname: Vorobjeva
authors.affiliation: Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Kolchanov
authors.affiliation: Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Klaus H
authors.initials: KH
authors.lastname: Kaestner
authors.affiliation: 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.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
mesh_terms: D000818:Animals; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics; D020869:Gene Expression Profiling; D016678:Genome; D007515:Islets of Langerhans / Q000378:metabolism*; D051379:Mice; D016688:Mice, Inbred NOD; D046228:Microarray Analysis / Q000379:methods*; D010179:Pancreas / Q000378:metabolism*; D011506:Proteins / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D011506:Proteins