Identifying nonspecific SAGE tags by context of gene expression.

Xijin Ge, San Ming Wang

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Many serial analysis of gene expression (SAGE) tags can be matched to multiple genes, leading to difficulty in SAGE data interpretation and analysis. As only a subset of genes in the human genome are transcribed in a certain type of tissue/cell, we used microarray expression data from different tissue types to define contexts of gene expression and to annotate SAGE tags collected from the same or similar tissue sources. To predict the original transcript contributing a nonspecific SAGE tag collected from a particular tissue, we ranked the corresponding genes by their expression levels determined by microarray. We developed a tissue-specific SAGE tag annotation database based on microarray data collected from 73 normal human tissues and 18 cancer tissues and cell lines. The database can be queried online at: http://www.basic.northwestern.edu/SAGE/. The accuracy of this database was confirmed by experimental data.

Original languageEnglish (US)
Pages (from-to)199-204
Number of pages6
JournalMethods in molecular biology (Clifton, N.J.)
Volume387
DOIs
StatePublished - 2008

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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