Prediction of cell type-specific gene modules: identification and initial characterization of a core set of smooth muscle-specific genes.
Artikel i vetenskaplig tidskrift, 2003

Genes that are expressed in the same subset of cells potentially constitute a module regulated by shared cis-regulatory elements and a distinct set of transcription factors. Identifying such units is an important entry point to the molecular study of cell differentiation. We developed a general method to classify cell type-specific genes from expressed sequence tag (EST) data, and we optimized it for identification of smooth muscle cell (SMC)-specific genes. Expression profiles were derived from the quantitative distribution of EST data in mouse, and genes were classified based on their profile similarity to known reference genes, in this case smooth muscle myosin heavy chain. A large majority (>90%) of known SMC-specific genes were identified, together with novel candidates. Extensive experimental validation confirmed SMC-specific expression of candidates, for example, lipoma preferred partner (LPP) and a novel SMC-specific putative monoamine oxidase, SMAO. Our method performed considerably better than other computational methods in an objective cross validation comparison. The total number of SMC-specific genes is estimated to be approximately 50.

embryology

cytology

statistics & numerical data

genetics

Lens

Gene Expression Regulation

Smooth

Organ Specificity

chemistry

Smooth

Expressed Sequence Tags

Retina

Databases

genetics

Genetic

Mice

Crystalline

Genetic Markers

Muscle

In Situ Hybridization

cytology

Animals

Computational Biology

embryology

Genome

chemistry

Vascular

Gene Expression Profiling

Myosin Heavy Chains

embryology

cytology

Research Design

cytology

chemistry

Predictive Value of Tests

Muscle

Författare

Sven Nelander

Göteborgs universitet

Petter Mostad

Chalmers, Institutionen för matematisk statistik

Göteborgs universitet

Per Lindahl

Göteborgs universitet

Genome Research

1088-9051 (ISSN) 1549-5469 (eISSN)

Vol. 13 8 1838-54

Ämneskategorier

MEDICIN OCH HÄLSOVETENSKAP

DOI

10.1101/gr.1197303

PubMed

12869577