Identification of Monotonically Differentially Expressed Genes for IFN-β-Treated Multiple Sclerosis Patients

Table 2

MEGs identified by the proposed method.

Responders						Nonresponders
“Good response” genes			“Bad response” genes			“Bad response” genes
Symbol	MEG	DEG	Symbol	MEG	DEG	Symbol	MEG	DEG
AFTPH	↑	↓	AGFG1	↑	↑	NAP1L4	↓	↓
ALOX5	↑	↓	CHM	↑	↑	MMS19	↓	↓
ATG7	↑	↓	IGLL1	↓	↓
MYD88	↑	↓	PELI1	↑	↑
LILRB1	↑	↓	PTEN	↑	↑
PRKAB1	↑	↓
PSEN1	↑	↓
VAMP3	↑	↓

MEGs ↑: monotonically increasing genes over time; MEGs ↓: monotonically decreasing genes over time; DEGs ↑: overexpressed genes (MS versus control); DEGs ↓: underexpressed genes (MS versus control). For the discordant genes, the directions of monotonic expression change and differential expression change are opposite to each other; over a period of time, the gene expression values tend to return to the expression levels of normal controls. For the concordant genes, the directions of monotonic expression change and differential expression change are identical to each other; over a period of time, the gene expression values tend to deviate more away from the expression levels of normal controls.