RT Journal
A1 Nelander, Sven
A1 Mostad, Petter
A1 Lindahl, Per
T1 Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes
JF Genome Research 
JO Genome Research 
YR 2003 
FD August 01 
VO 13 
IS 8 
SP 1838 
OP 1854 
DO 10.1101/gr.1197303 
UL http://genome.cshlp.org/content/13/8/1838.abstract 
AB 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 ∼50.