TNF and rheumatoid arthritis: The RA-perturbed networks revealed that 1) RA FLS act as a major player responsible for various RA-perturbed processes, 2) anti-TNF-α therapy moves a wide spectrum of RA-perturbed processes toward normality, and 3) 19 key transcription factors (TFs) could play critical roles in the regulation of 55% of dysregulation encoded by the RA-perturbed networks.