A dedicated microarray for in-depth analysis of pre-mRNA splicing events: application to the study of genes involved in the response to targeted anticancer therapies

Pesson, Marine; Eymin, Béatrice; De La Grange, Pierre; Simon, Brigitte; Corcos, Laurent

doi:10.1186/1476-4598-13-9

Molecular Cancer

Table 2 Deregulated probe sets in SRSF2-over-expressing H358 lung adenocarcinoma cells

From: A dedicated microarray for in-depth analysis of pre-mRNA splicing events: application to the study of genes involved in the response to targeted anticancer therapies

Gene symbol	Region name	Region type	Confidence	Regulation	Fold-change	P-value	RT-PCR
AKT2	je14_e15_5p_region	Junction	Low	Down	1.63	1.36E-02	No
*AKT3*	je7_e8	Junction	High	Down	5.99	2.07E-05	Yes
*AKT3*	e8	Exon	High	Down	4.19	4.10E-03	Yes
*HER1/EGFR*	je16_e19	Junction	High	Down	3.66	1.42E-03	Yes
HER1/EGFR	predict_exon_1_2-10	Exon	Medium	Up	33.98	0.00E + 00	No
HER1/EGFR	est_1_2	Exon	Medium	Up	17.35	1.00E-09	No
HER1/EGFR	predict_exon_2_3-1	Exon	Medium	Up	4.97	5.51E-05	No
HER1/EGFR	e26	Exon	Medium	Down	2.64	2.30E-03	No
HER1/EGFR	ae1_donor_alter	Donor_alter	Medium	Up	5.55	5.40E-03	No
HER1/EGFR	je14_e15	Junction	Low	Down	1.87	1.05E-02	No
HER1/EGFR	je12_e13	Junction	Low	Down	1.76	1.13E-02	No
HER2	ae10_prom_alter	Prom_alter	Medium	Down	2.73	2.32E-02	No
HER3	je22_ae23_acceptor_alter_l	Junction	Low	Up	1.68	3.33E-02	No
*HIF1A*	je10_e11	junction	High	Down	1.87	1.66E-05	Yes
*HIF1A*	e10	Exon	High	Down	1.62	3.65E-02	Yes
*HIF1A*	e9	Exon	High	Down	1.56	4.78E-02	Yes
HIF1A	e5	Exon	Low	Down	2.07	1.23E-02	No
HIF1A	je1_5p_region_ae3_acceptor_alter	Junction	Low	Down	1.56	1.64E-02	No
HIF1A	je14_e16	Junction	Low	Up	2.22	2.08E-02	No
PIK3R2	e6	Exon	High	Down	1.97	7.61E-05	No
PIK3R2	je5_e6	Junction	High	Down	3.95	3.98E-04	No
PIK3R2	je7_e8	Junction	Low	Down	1.68	2.14E-03	No
PIK3R2	e9	Exon	Low	Down	1.74	3.34E-03	No
PIK3R2	je2_e3	Junction	Low	Down	1.58	4.36E-02	No
*VEGFA*	e4_term_alter	Term_alter	High	Up	10.18	7.43E-08	Yes
*VEGFA*	ae6_donor_alter_2	Donor_alter	High	Down	2.44	4.18E-07	Yes
*VEGFA*	jae6_donor_alter_2_e7	Junction	High	Down	1.93	4.96E-03	Yes
*VEGFA*	ae7_donor_alter	Donor_alter	High	Up	1.80	6.98E-04	Yes
VEGFA	e7	Exon	Low	Up	1.50	4.00E-04	No
VEGFB	je2_e3	Junction	Low	Down	1.62	6.47E-05	No

A list of the 30 differentially expressed and deregulated custom probe sets (≥ 1.5 FC, P-value ≤ 0.05) from expressed genes among the 16 analyzed genes in SRSF2-over-expressing lung cancer cells in comparison to control cells on the 15 k custom microarray is presented. The regulations were associated with a high, medium or low confidence, depending on the regulation of probes in the vicinity of the deregulated probe sets. According to the results with a high confidence (in bold characters), we expect an up-regulation of exon 7 and a down-regulation of exon 8 for AKT3, a multiple exon skipping for HER1/EGFR, a skipping of both exons 9 and 10 for HIF1A, an alternative polyadenylation in intron 4, and alternative donor sites for exons 6 and 7 for VEGFA.

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ISSN: 1476-4598

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