Table 1.

Overlapping DEGs identified in UPF3B patients and previous microarray studies of different NMD-deficient cell lines

Reference	NMD-deficient models	Reported probesets	Expressed in LCL	DEGs (This study)	Gene symbol	Gene assignment	Fold change (RNA-SEQ)	Fold change (exon array)
Chan et al.10	UPF3B and UPF3A KD in HeLa cell by shRNA	44	25	2	ARHGAP24	Rho GTPase-activating protein 24	2.4	3.0
					MCTP2	Multiple C2 domains, transmembrane 2	3.6	4.3
Chan et al.9	UPF3B KD in Hela cell by shRNA	94	42	2	GBP1	Guanylate-binding protein 1	5.4	1.6
					MAN1A1	Mannosidase alpha class 1A	2.3	1.7
	UPF1 KD in Hela cell by shRNA	66	32	2	MACROD2	MACRO domain-containing 2	4.4	1.0
					ETV5	ETS variant gene 5	2.6	1.7
Mendell et al.12	UPFl KD in HeLa cell by siRNA	197	168	5	TSC22D3	TSC22 domain family, member 3	2.6	1.4
					GABARAPL1	GABA(A) receptor-associated protein- like 1	3.0	1.1
					KLHL21	Kelch-like 21 (Drosophila)	2.0	1.1
					SAT1	Spermidine N1-acetytransferase	2.0	1.5
					PHGDH	Phosphoglycerate dehydrogenase	4.5	1.8
Wittmann et al.13	UPF2 KD in HeLa cell by siRNA	41	32	5	TSC22D3	TSC22 domain family, member 3	2.6	1.4
					MUC13	Mucin 13, epithelial transmembrane	2.6	3.0
					TSPAN12	Tetraspanin 12	2.0	2.0
					PDE4B	Phosphodiesterase 4B	2.4	1.3
					SCL12A7	Solute carrier family 12 (potassium/ chloride transporters), member 7	2.4	2.5
Weischenfeldt J et al.14	Upf2 KO in mouse bone marrow-derived macrophage	235	138	0
	Upf2 KO in mouse thymocytes	44	22	0
Rehwinkel et al.15	upf1, upf2 and upf3 KD in fly by siRNA	26	16	0
He et al.16	upf1, nmd2 and upf3 KO in yeast	61	15	0

Abbreviations: DEGs, differently expressed genes; KD, knockdown; KO, knockout; NMD, nonsense-mediated mRNA decay; shRNA, small hairpin RNA; siRNA, small-interfering RNA.

DEGs or orthologs (if found) were used for comparison. All of these studies employed the use of early microarray platforms namely Affymetrix HU133A Plus 2.0 ( × 2), HU133A, U95, U133, Mouse Genome 430 2.0, DrosGenome 1 and YG985, respectively.