The Genexpress IMAGE Knowledge Base of the Human Muscle Transcriptome: A Resource of Structural, Functional, and Positional Candidate Genes for Muscle Physiology and Pathologies

Abstract

Sequence, gene mapping, and expression data corresponding to 910 genes transcribed in human skeletal muscle have been integrated to form the muscle module of the Genexpress IMAGE Knowledge Base. Based on cDNA array hybridization, a set of 14 transcripts preferentially or specifically expressed in muscle have been selected and characterized in more detail: Their pattern of expression was confirmed by Northern blot analysis; their structure was further characterized by full-insert cDNA sequencing and cDNA extension; the map location of the corresponding genes was refined by radiation hybrid mapping. Five of the 14 selected genes appear as interesting positional and functional candidate genes to study in relation with muscle physiology and/or specific orphan muscular pathologies. One example is discussed in more detail. The expression profiling data and the associated Genexpress Index2 entries for the 910 genes and the detailed characterization of the 14 selected transcripts are available from a dedicated Web server athttp://idefix.upr420.vjf.cnrs.fr/IMAGE/Page_unique/welcome_muscles.html. The database has been organized to provide the users with a working space where they can find curated, annotated, integrated data for their genes of interest. Different navigation routes to exploit the resource are discussed.[Tables A and B are available as supplementary information at www.genome.org and also athttp://idefix.upr420.vjf.cnrs.fr/IMAGE/Page_unique/welcome_muscles.html.]

Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles

“…As the identity of each clone is unknown, we do not know for certain how representative is the porcine skeletal muscle cDNA microarray. On the one hand, considering that there might be fewer than 30,000 human genes [25], and assuming that 50% of all genes are transcriptionally active at one time in a given tissue [26], it is possible that around 20% of the genes that are expressed in skeletal muscle are found on our microarray [25,27]. On the other hand, a group of 4080 human skeletal muscle genes, which included both skeletal muscle-specific genes and genes expressed in skeletal muscle as well as in other tissues, was found to correspond to 80% of the total number of genes expressed in skeletal muscle as reported so far in Unigene (including foetal muscle and rhabdomyosarcoma) [26].…”

Fine mapping of a distinctive autosomal dominant vacuolar neuromyopathy using 11 novel microsatellite markers from chromosome band 19p13.3

“…5 Finally in mice, gene targeting inactivation of PTPRS causes severe neurologic defects including spastic movements, tremor, ataxia gait, abnormal limb flexion and defective proprioception. 5 GENX-3587 is a muscle-specific transcript that has been mapped within the disease-locus critical region by Pietù et al, 6 we also hypothesised its involvement in the disease pathogenesis. Although …”

Gene expression profiling of human satellite cells during muscular aging using cDNA arrays

“…More data on differential expression patterns must be generated and relevant aging markers, both in pre-senescence and in senescence, need to be identified. During the last decade, high-density cDNA arrays or microarrays have emerged as a tool to measure global gene expression in specific conditions in mice, human or other organisms such as C. elegans and yeast (Brown and Botstein, 1999;Pietu et al, 1999;Reinke, 2002). In order to investigate the variations of gene expression with increasing donor age and to identify new genes potentially involved in these process, muscular aging has been studied using human satellite cells isolated from skeletal muscles of 5-day-old, 52-year-old and 79-year-old individuals.…”