Extraocular muscle is defined by a fundamentally distinct gene expression profile

Skeletal muscle fibers are defined by patterned covariation of key traits t hat determine contractile and metabolic characteristics. Although the funct ional properties of most skeletal muscles result from their proportional co ntent of a few conserved muscle fiber types, some, typically craniofacial, muscles exhibit fiber types that appear to lie outside the common phenotypi c range. We analyzed gene expression profiles of three putative muscle clas ses, limb, masticatory, and extraocular muscle (EOM), in adult mice by high -density oligonucleotide arrays. Pairwise comparisons using conservative ac ceptance criteria identified expression differences in 287 genes between EO M and limb and/or masticatory muscles. Use of significance analysis of micr oarrays methodology identified up to 400 genes as having an EOM-specific ex pression pattern. Genes differentially expressed in EOM reflect key aspects of muscle biology, including transcriptional regulation, sarcomeric organi zation, excitation-contraction coupling, intermediary metabolism, and immun e response. These patterned differences in gene expression define EOM as a distinct muscle class and may explain the unique response of these muscles in neuromuscular diseases.