Figure 1

Normalization, filtering, SAFE, LIMMA and SAM analyses of lymphocyte-derived microarray data from ALS patients and healthy controls. Microarray analyses were performed on purified PBLs isolated from patients affected by sporadic amyotrophic lateral sclerosis (sALS) (n = 11) and healthy control subjects (HCs) (n = 11). The dual color mode in the common reference design was used to interrogate the expression of ~40000 transcripts (~30000 unique genes) using Agilent Human Whole Genome 4 × 44k Microarrays. Raw expression data were normalized and filtered using the MIDAS pipeline in the TM4 microarray suite (TIGR Genomics, Rockville, MD) to generate the dataset DS7000. SAFE was used for testing enrichment of functional gene ontology (GO) categories related to biological processes, molecular functions, cellular components, protein families (Pfam) and the KEGG databases. DS7000 was subjected to LIMMA and SAM analyses using TM4/TMeV v4.5.1 to determine differentially expressed (DE) genes. The online tool Data Overlapping and Area-Proportional Venn Diagram (http://bioinforx.com/free/bxarrays/overlap.php) was used to generate the Venn diagram.