Large Scale Dataset: Human Muscle Disease Tissues from ExpressionAtlas

This set includes differentially expressed gene lists for 10 muscle diseases, taken from the experiment “Transcription profiling by array of 12 human muscle diseases” that was deposited and analyzed in the Expression Atlas database (http://www.ebi.ac.uk/gxa/home). This experiment is based on GSE3307 and identified the most differentially expressed genes in 12 muscle diseases in comparison to control skeletal muscle cells. The diseases analyzed in this experiment are:

1. Limb-Girdle Muscular Dystrophy Type 2i (LGMD-2I)
2. Limb-Girdle Muscular Dystrophy, Type 2b (LGMD-2B)
3. Calpainopathy (LGMD-2A)
4. Duchenne Muscular Dystrophy (DMD)
5. Emery-Dreifuss Muscular Dystrophy, Dominant Type (EDMD-AD)
6. Emery-Dreifuss Muscular Dystrophy, X-Linked (EDMD-XR)
7. Becker Muscular Dystrophy (BMD)
8. Childhood Type Dermatomyositis (JDM)
9. Hereditary Spastic Paraplegia (HSP)
10. Facioscapulohumeral Muscular Dystrophy (FSHD)

In the original experiment, skeletal muscle tissues from acute quadriplegic myopathy (AQM) and amyotrophic lateral sclerosis (ALS) patients were also analyzed, but this data is not included in this gene set.

These lists were prepared as following:

• Array data was normalized by the RMA method using Oligo version 1.24.2.
• Moderated t-statistics were computed with Limma version 3.16.8 and independent filtering performed using genefilter version 1.46.1, with gene variances as filter statistic. P-values were than adjusted using Benjamini & Hochberg (1995) FDR correction.
• Genes were defined as differentially expressed if they have fold change larger than 2 and their adjusted p-value is lower or equal to 0.05. If more than 200 genes pass this threshold, the top 200 up- and down-regulated genes are presented.