Fig. 1

Naming convention for Muscle Gene Sets. Each name was chosen to be both succinct and readily understandable. This was not an automated process—consideration was given to the name of each gene set. The first segment, before the triple underscore, has the generic form ‘up_in_Group1_v_Group2’ or ‘down_in_Group1_v_Group2’, referring to genes that were up- or downregulated in the comparison of group 1 (e.g. mdx) to group 2 (e.g. WT), for which ‘up’ indicates greater expression in group1 compared to group2, and ‘down’ means lesser expression in group1. Following the triple underscore, species name is then given, then age/timepoint and/or tissue description and/or gender (in any order). Finally, each gene set is given a MGS ID number. List of time abbreviations used: h = hour(s); d = day(s); wk. = week(s); mo = month(s); y = year(s). List of other abbreviation conventions used (ordered by appearance in the complete MGS gmt file): ctl = control; WT = wild-type; gastroc/gastr = gastrocnemius muscle; DMD = Duchenne muscular dystrophy; quad = quadriceps muscle; skel = skeletal; dysf = dysferlinopathy; EDMD = Emery-Dreifuss muscular dystrophy; EDL = extensor digitorum longus muscle; TA/tib_anterior = tibialis anterior muscle; diff = differentiation/differentiated (of myotubes); prim = primary cells; vast_lat/vastus_lat = vastus lateralis; KO = knock-out; mir = microRNA. Some study-specific abbreviations are used, which are assumed to be understandable from context or occasionally requiring reference to the source GEO entry indicated in the information column of the gmt file