Schematic representation of the data analysis and data visualization pipeline. Designed for unbiased mapping of alterations in the transcriptional landscape of the extracellular milieu (EM). CONNECTIVITY, degree of overlap in LE-members between the GSs the edge is connecting; FDR, false discovery rate; GS, gene set; KEGG, Kyoto Encyclopedia of Genes and Genomes; LE, leading edge; LIST, percentage of genes in the ranked gene list before (for positive enrichment score (ES)) or after (for negative ES) the peak in the running ES (indication of where in the list the enrichment score is attained); MCL, Markov cluster algorithm; NCI, National Cancer Institute database; PFAM, Pfam protein families database ; SAM, significance analysis of microarrays; SG, salivary gland; SIGNAL, ES strength that combines LIST and TAGS; TAGS, percentage of gene hits before (for positive ES) or after (for negative ES) the peak in the running ES, (indicates percentage of genes contributing to ES).
Delaleu et al. Arthritis Research & Therapy 2013 15:R174 doi:10.1186/ar4362