Novel genes identified by manual annotation and microarray expression analysis in the pancreas.
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.
Mazzarelli
Joan M
JM
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.
White
Peter
P
Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Gorski
Regina
R
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.
Brestelli
John
J
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.
Pinney
Deborah F
DF
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.
Arsenlis
Athanasios
A
Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Katokhin
Alexey
A
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Belova
Olga
O
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Bogdanova
Vera
V
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Elisafenko
Eugenij
E
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Gubina
Marina
M
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Nizolenko
Lilia
L
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Perelman
Polina
P
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Puzakov
Mikhail
M
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Shilov
Alexandre
A
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Trifonoff
Vladimir
V
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Vorobjeva
Nadezhda
N
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Kolchanov
Nikolay
N
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
Kaestner
Klaus H
KH
Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Stoeckert
Christian J
CJ
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.
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
D018076:DNA, Complementary; D011506:Proteins