A large quantity of novel human antisense transcripts detected by LongSAGE

Xijin Ge, Qingfa Wu, Yong Chul Jung, Jun Chen, San Ming Wang

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2475-2479
Number of pages5
JournalBioinformatics
Volume22
Issue number20
DOIs
StatePublished - Oct 1 2006

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Databases
Genes
Forensic Anthropology
Messenger RNA
Chromosome Mapping
Expressed Sequence Tags
Human Genome
Genome
Sensitivity and Specificity
Chemical analysis
Human
Quantitative Analysis
Specificity
Experimental Results
Demonstrate

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

A large quantity of novel human antisense transcripts detected by LongSAGE. / Ge, Xijin; Wu, Qingfa; Jung, Yong Chul; Chen, Jun; Wang, San Ming.

In: Bioinformatics, Vol. 22, No. 20, 01.10.2006, p. 2475-2479.

Research output: Contribution to journalArticle

Ge, Xijin ; Wu, Qingfa ; Jung, Yong Chul ; Chen, Jun ; Wang, San Ming. / A large quantity of novel human antisense transcripts detected by LongSAGE. In: Bioinformatics. 2006 ; Vol. 22, No. 20. pp. 2475-2479.
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