Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

BMC Bioinformatics

Table 5 LocusIDs and probe sets corresponding to the ten largest z-score variances for the NGF data set.

Z-score Variance	LocusID	Gene Symbol	Probe set ID	Z-score	Affymetrix Annotation Grade (Apr/06) [7]	Comments
103.8	25513	Pik3r1	1370114_a_at	-8.577	A	error
			1371776_a_at	5.83	E
33.4	363087	RGD1560364_predicted	1376129_at	3.837	E	error, opposite strands
			1380038_at	-4.34	B
17.0	298530	RGD1308209_predicted	1370876_at	1.788	C	error, different chromosomes
			1376841_at	-4.046	E
13.6	24737	RT1-Aw2 (MHC Class I antigen)	1369110_x_at	1.447	A
			1370428_x_at	2.057	A
			1370429_at	3.397	A
			1370463_x_at	-4.724	-
			1370972_x_at	0.573	-
			1371078_at	3.449	B
			1371111_at	0.515	-
			1371119_at	0.796	-
			1371171_at	-0.398	A
			1371209_at	7.035	-
			1371210_s_at	1.582	A
			1371213_at	1.965	-
			1388071_x_at	4.308	A
			1388202_at	-7.565	A
			1388203_x_at	-6.808	B
			1388236_x_at	-0.588	-
			1388254_a_at	-0.57	-
			1388255_x_at	4.886	-
			1388256_at	-0.335	-
			1388694_at	5.334	-
			1389734_x_at	0.967	B
13.2	116561	Cltb	1367907_a_at	1.71	A	error, 1375324_at, wrong strand
			1375324_at	-3.437	E
13.0	171454	Btbd14b	1371826_at	2.191	E	1371826_at, 1.5 kb beyond 3' end of RefSeq sequence
			1387443_at	7.287	A
12.9	24225	Bdnf	1368677_at	6.115	A	alt. poly(A) sites;
			1368678_at	1.034	A	1368678_at last 4 probes don't align to genomic sequence
12.2	311846	Lrrc8_predicted	1374296_at	1.116	E	error
			1382920_at	6.06	A
12.1	64160	Basp1	1369310_at	3.803	A	1375143_at – error, wrong strand;
			1375143_at	9.602	E
			1398350_at	3.391	C	1398350_at – beyond 3' end of RefSeq
11.8	25601	Oprm1	1369109_at	4.617	A	alt. splicing
			1387461_at	-0.235	A

ISSN: 1471-2105