Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues.

Lei Qian, Yunlong Liu, Hui (Herb) Sun, Hiroki Yokota

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The availability of human genome sequences provides life scientists and biomedical engineers with a challenging opportunity to develop computational and experimental tools for quantitatively analyzing biological processes. In response to a growing need to integrate experimental mRNA expression data with human genome sequences, we present here a unique analysis named "Promoter-Based Estimation (PROBE)" analysis. The PROBE analysis is "systems analysis" of transcriptional processes using control and estimation theories. A linear model was built in order to estimate the mRNA levels of a group of genes from their regulatory DNA sequences. The model was also used to interpret two independent datasets in skeletal tissues. The results demonstrated that the mRNA levels of a family of matrix metalloproteinases can be modeled from a distribution of cis-acting elements on regulatory DNA sequences. The model accurately predicted a stimulatory role of cis-acting elements such as AP1, NFY, PEA3, and Sp1 as well as an inhibitory role of AP2. These predictions are consistent with biological observations, and a specific assay for testing such predictions is proposed. Although eukaryotic transcription is a complex mechanism, the two examples presented here support the potential use of the described analysis for elucidating the functional significance of DNA regulatory elements.

Original languageEnglish (US)
JournalFrontiers in Bioscience
Volume7
StatePublished - 2002
Externally publishedYes

Fingerprint

Systems Analysis
Matrix Metalloproteinases
Genes
DNA sequences
Systems analysis
Human Genome
Tissue
Messenger RNA
Biological Phenomena
Transcription
Regulator Genes
Process control
Linear Models
Assays
Availability
Engineers
DNA
Testing

Cite this

Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues. / Qian, Lei; Liu, Yunlong; Sun, Hui (Herb); Yokota, Hiroki.

In: Frontiers in Bioscience, Vol. 7, 2002.

Research output: Contribution to journalArticle

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