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Annotating nonspecific SAGE tags with microarray data.

Publication ,  Journal Article
Ge, X; Jung, Y-C; Wu, Q; Kibbe, WA; Wang, SM
Published in: Genomics
January 2006

SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags.

Duke Scholars

Published In

Genomics

DOI

ISSN

0888-7543

Publication Date

January 2006

Volume

87

Issue

1

Start / End Page

173 / 180

Location

United States

Related Subject Headings

  • Sequence Tagged Sites
  • Oligonucleotide Array Sequence Analysis
  • Neoplasms
  • Multigene Family
  • Humans
  • Genetics & Heredity
  • Gene Expression Regulation
  • Gene Expression Profiling
  • Databases, Genetic
  • Cell Line
 

Citation

APA
Chicago
ICMJE
MLA
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Ge, X., Jung, Y.-C., Wu, Q., Kibbe, W. A., & Wang, S. M. (2006). Annotating nonspecific SAGE tags with microarray data. Genomics, 87(1), 173–180. https://doi.org/10.1016/j.ygeno.2005.08.014
Ge, Xijin, Yong-Chul Jung, Qingfa Wu, Warren A. Kibbe, and San Ming Wang. “Annotating nonspecific SAGE tags with microarray data.Genomics 87, no. 1 (January 2006): 173–80. https://doi.org/10.1016/j.ygeno.2005.08.014.
Ge X, Jung Y-C, Wu Q, Kibbe WA, Wang SM. Annotating nonspecific SAGE tags with microarray data. Genomics. 2006 Jan;87(1):173–80.
Ge, Xijin, et al. “Annotating nonspecific SAGE tags with microarray data.Genomics, vol. 87, no. 1, Jan. 2006, pp. 173–80. Pubmed, doi:10.1016/j.ygeno.2005.08.014.
Ge X, Jung Y-C, Wu Q, Kibbe WA, Wang SM. Annotating nonspecific SAGE tags with microarray data. Genomics. 2006 Jan;87(1):173–180.
Journal cover image

Published In

Genomics

DOI

ISSN

0888-7543

Publication Date

January 2006

Volume

87

Issue

1

Start / End Page

173 / 180

Location

United States

Related Subject Headings

  • Sequence Tagged Sites
  • Oligonucleotide Array Sequence Analysis
  • Neoplasms
  • Multigene Family
  • Humans
  • Genetics & Heredity
  • Gene Expression Regulation
  • Gene Expression Profiling
  • Databases, Genetic
  • Cell Line