Abstract: Neurodegenerative diseases that affect the motor neurons, including amyotrophic lateral sclerosis (ALS), have little treatment options and are generally rapidly fatal (1, 2). We harnessed the power of unbiased, whole transcriptome differential gene expression analysis, utilizing primary patient cells and tissues to discover genes whose expression defines ALS using published and public data (3, 4). We found significant differential expression of HOXC9, encoding homeobox C9, in the skeletal muscle of patients with ALS. HOXC9 was also differentially expressed in the induced pluripotent stem cell (iPSC)-derived motor neurons of patients with ALS. HOXC9 transcript was present at significantly lower levels in ALS patient skeletal muscle as compared to control skeletal muscle. These analyses will begin to define the transcriptional landscape of ALS.