Principal component analysis from all scenarios. There is a clear distinction between healthy samples and systemic lupus erythematosus (SLE) patients, shown in blue and red, respectively. (A) Scenario I. (B) Scenario II. (C) Scenario III. (D) Scenario IV. The Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) scores indicate that most SLE patients exhibiting close to normal gene expression are in remission (SLEDAI score 0) or have low disease activity (SLEDAI scores 2 and 3).