Quantitative gene expression profiles in real time from expressed sequence tag databases.
An accumulation of expressed sequence tag (EST) data in the public domain and the availability of bioinformatic programs have made EST gene expression profiling a common practice. However, the utility and validity of using EST databases (e.g., dbEST) has been criticized, particularly for quantitative assessment of gene expression. Problems with EST sequencing errors, library construction, EST annotation, and multiple paralogs make generation of specific and sensitive qualitative arid quantitative expression profiles a concern. In addition, most EST-derived expression data exists in previously assembled databases. The Virtual Northern Blot (VNB) (http: //tlab.bu.edu/vnb.html) allows generation, evaluation, and optimization of expression profiles in real time, which is especially important for alternatively spliced, novel, or poorly characterized genes. Representative gene families with variable nucleotide sequence identity, tissue specificity, and levels of expression (bcl-xl, aldoA, and cyp2d9) are used to assess the quality of VNB's output. The profiles generated by VNB are more sensitive and specific than those constructed with ESTs listed in preindexed databases at UCSC and NCBI. Moreover, quantitative expression profiles produced by VNB are comparable to quantization obtained from Northern blots and qPCR. The VNB pipeline generates real-time gene expression profiles for single-gene queries that are both qualitatively and quantitatively reliable.
Funari
Vincent A
VA
*Biology Department, Boston University, Boston, MA 02215, USA.
Voevodski
Konstantin
K
Leyfer
Dimitry
D
Yerkes
Laura
L
Cramer
Donald
D
Tolan
Dean R
DR
D015152:Blotting, Northern; D019295:Computational Biology; D017931:DNA Primers; D016208:Databases, Factual; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D005819:Genetic Markers / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012680:Sensitivity and Specificity
D017931:DNA Primers; D005819:Genetic Markers