Advanced spot quality analysis in two-colour microarray experiments

BMC Research Notes

Table 4 Comparison of MAIA and GP spot filtering approaches on a set of 24 selected genes confirmed by RT-PCR or qRT-PCR.

Symbol	Description	MAIA	GP-standard	GP-weak	GP-medium	GP-strong
	Down
KLF5	Krueppel-like factor 5	+	+	+	+
TJP3	Tight junction protein ZO-3	+	+	+
KRT12	Keratin, type I cytoskeletal 12	+	+	+
BSPRY	B-box and SPRY domain containing	+		+
CORO1A	Coronin-1A	+	+	+	+
STAP2_HUMAN	Signal-transducing adaptor protein 2	+		+
PPP1R16A	Protein phosphatase 1 regulatory subunit 16A	+	+	+	+	+
KRT18	Keratin, type I cytoskeletal 18	+
STMN3	Stathmin-3	+	+	+	+
TRIB3	Tribbles homolog 3	+		+
CLDN3	Claudin-3	+
TXNIP	Thioredoxin interacting protein	+
	Up
MSX1	Homeobox protein MSX-1	+	+	+	+
GULP1	GULP, engulfment adaptor PTB domain containing 1	+	+	+	+
DUSP2	Dual specificity protein phosphatase 2	+	+	+	+
ID3	DNA-binding protein inhibitor ID-3	+
THBD	Thrombomodulin precursor	+	+	+
HS6ST2	Heparan sulfate 6-O-sulfotransferase 2	+	+	+
TGFBI	Transforming growth factor-beta-induced protein ig-h3 precursor	+
S 100A 10	Calpactin I light chain	+
SERPINH1	Collagen-binding protein 2 precursor	+
SNAI2	Zinc finger protein SLUG	+	+	+
COL5A1	Collagen alpha 1(V) chain precursor	+	+	+	+
ANXA2	Annexin A2	+	+	+	+	+

RT-PCR and qRT-PCR analysis of 24 selected genes was performed to validate microarray data. Then, the presence of these genes in lists of DE genes obtained in the whole-genome microarray experiment was determined using different spot quality evaluation approaches in MAIA and GP. Fourteen genes were detected using the GP-standard conditions, 17, 9, 2 were present in the GP-weak, GP-medium, GP-strong lists, correspondingly. All 24 genes were found in the MAIA DE gene list. The sign "+" indicates if a gene is present in the corresponding DE gene list.

ISSN: 1756-0500