TY  - JOUR
A1  - Kampa, Dione
A1  - Cheng, Jill
A1  - Kapranov, Philipp
A1  - Yamanaka, Mark
A1  - Brubaker, Shane
A1  - Cawley, Simon
A1  - Drenkow, Jorg
A1  - Piccolboni, Antonio
A1  - Bekiranov, Stefan
A1  - Helt, Gregg
A1  - Tammana, Hari
A1  - Gingeras, Thomas R.
T1  - Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
Y1  - 2004/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 331 
EP  - 342 
DO  - 10.1101/gr.2094104 
VL  - 14 
IS  - 3 
UR  - http://genome.cshlp.org/content/14/3/331.abstract 
N2  - In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density oligonucleotide arrays on cytosolic poly(A)+ RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas an additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and up to 21% of known genes have only a single isoform based on exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with an identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of any known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation in expression than the well-characterized genes. Novel transcripts were further characterized based on their distance to annotations, transcript size, coding capacity, and identification as antisense to intronic sequences. By RT-PCR, 126 novel transcripts were independently verified, resulting in a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for “gene” to encompass these growing, novel classes of RNA transcripts in the human genome. 
ER  -