Unlike gene expression

The manifestation of autoantibodies is fundamentally different than gene expression, generating very different data. The fundamental assumptions underlying bioinformatics pipelines designed for gene expression analysis do not necessarily apply to autoantibody analysis.

AutoantibodiesGene Expression
Variability in the populationHigh
from patient to patient and within populations
from patient to patient and within populations
Data comparisonBinary
Present or Absent
Upregulated > Unchanged > Downregulated
Frequency of hitsLow
Only a small percentage (10%–30%) of a population will be positive for a given autoantibody
Gene expression occurs at a high frequency in a population. Finding a gene that is upregulated or downregulated in a large portion of the population is common.