A large quantity of novel human antisense transcripts detected by LongSAGE
- PMID: 16895931
- DOI: 10.1093/bioinformatics/btl429
A large quantity of novel human antisense transcripts detected by LongSAGE
Abstract
Motivation: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632 813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts.
Results: Our study identified 45 321 tags that match the antisense strand of 9804 known mRNA sequences, 6606 of which contain antisense ESTs and 3198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database.
Conclusions: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome.
Similar articles
-
Unexpected observations after mapping LongSAGE tags to the human genome.BMC Bioinformatics. 2007 May 15;8:154. doi: 10.1186/1471-2105-8-154. BMC Bioinformatics. 2007. PMID: 17504516 Free PMC article.
-
Widespread occurrence of antisense transcription in the human genome.Nat Biotechnol. 2003 Apr;21(4):379-86. doi: 10.1038/nbt808. Epub 2003 Mar 17. Nat Biotechnol. 2003. PMID: 12640466
-
Transcriptional profile of rat extraocular muscle by serial analysis of gene expression.Invest Ophthalmol Vis Sci. 2002 Apr;43(4):1048-58. Invest Ophthalmol Vis Sci. 2002. PMID: 11923246
-
Gene identification through large-scale EST sequence processing.Appl Bioinformatics. 2003;2(3):123-9. Appl Bioinformatics. 2003. PMID: 15130797 Review.
-
Tag-based approaches for transcriptome research and genome annotation.Nat Methods. 2005 Jul;2(7):495-502. doi: 10.1038/nmeth768. Nat Methods. 2005. PMID: 15973418 Review.
Cited by
-
Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells.RNA. 2008 Oct;14(10):2030-7. doi: 10.1261/rna.1084308. RNA. 2008. PMID: 18820242 Free PMC article.
-
Triplet repeat-derived siRNAs enhance RNA-mediated toxicity in a Drosophila model for myotonic dystrophy.PLoS Genet. 2011 Mar;7(3):e1001340. doi: 10.1371/journal.pgen.1001340. Epub 2011 Mar 17. PLoS Genet. 2011. PMID: 21437269 Free PMC article.
-
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.Nucleic Acids Res. 2010 Jan;38(2):534-47. doi: 10.1093/nar/gkp954. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906709 Free PMC article.
-
Unexpected observations after mapping LongSAGE tags to the human genome.BMC Bioinformatics. 2007 May 15;8:154. doi: 10.1186/1471-2105-8-154. BMC Bioinformatics. 2007. PMID: 17504516 Free PMC article.
-
Generation of a non-small cell lung cancer transcriptome microarray.BMC Med Genomics. 2008 May 30;1:20. doi: 10.1186/1755-8794-1-20. BMC Med Genomics. 2008. PMID: 18513400 Free PMC article.
Publication types
MeSH terms
Substances
Associated data
- Actions
- Actions
- Actions
- Actions
LinkOut - more resources
Full Text Sources
Research Materials
