Global transcriptional responses to cisplatin in Dictyostelium discoideum identify potential drug targets

Van Driessche et al10.1073/pnas.0705996104XXYYYYY103.

Supporting Information

Files in this Data Supplement:

SI Table 2
SI Table 3
SI Table 4
SI Table 5
SI Table 6
SI Table 7
SI Table 8

Table 2. RT-PCR of microarray data from wild-type cells

Gene name	DDB no.	Fold change*		P value^†
Gene name	DDB no.	0 mM cisplatin	300 mM cisplatin	P value^†
abcB1	DDB0201666	0.77 ± 0.12	0.29 ± 0.11	0.0007
abcF4	DDB0191119	0.89 ± 0.07	0.38 ± 0.07	0.0323
abcG10	DDB0214895	0.71 ± 0.16	0.20 ± 0.02	0.0800
abcG21	DDB0191239	0.88 ± 0.07	0.35 ± 0.01	0.0142
alyB	DDB0231278	0.83 ± 0.12	2.98 ± 1.08	0.1760
amtA	DDB0185017	0.66 ± 0.18	4.91 ± 2.19	0.1948
atg8	DDB0191413	0.63 ± 0.21	0.13 ± 0.01	0.1384
bzpH	DDB0220095	0.69 ± 0.16	0.18 ± 0.05	0.0444
cycB	DDB0185035	0.72 ± 0.14	6.68 ± 1.19	0.0454
cprE	DDB0185092	0.83 ± 0.09	2.41 ± 0.59	0.0901
dnmA	DDB0187754	0.81 ± 0.11	0.29 ± 0.02	0.0585
repD	DDB0191272	0.81 ± 0.10	0.17 ± 0.02	0.0285
ubpA	DDB0231492	0.57 ± 0.22	0.09 ± 0.03	0.1964

*The data are averages and standard errors of three independent experiments, each done in triplicate.

^†From a two-tailed t test.

Table 3. RT-PCR of microarray data from wild-type and mutant strains

Gene name	DDB no.	Fold change*						P value^†
		AX4		sglA^-		sgkA^OE		P value^†
		0 mM cisplatin	300 mM cisplatin	0 mM cisplatin	300 mM cisplatin	0 mM cisplatin	300 mM cisplatin	Genotype	Treatment
abcF4	DDB0191119	0.64 ± 0.10	0.10 ± 0.02	1.04 ± 0.40	0.62 ± 0.09	0.56 ± 0.06	1.04 ± 0.29	0.094	0.395
aprA	DDB0231036	0.51 ± 0.12	1.49 ± 0.25	0.09 ± 0.03	0.25 ± 0.07	0.10 ± 0.01	0.34 ± 0.05	3.8E-07	2.0E-04
N/A	DDB0188863	0.28 ± 0.15	6.84 ± 1.56	0.02 ± 0.00	0.53 ± 0.18	0.02 ± 0.00	0.10 ± 0.02	0.001	0.003
ddiA	DDB0230141	0.38 ± 0.13	3.84 ± 1.20	0.02 ± 0.00	2.64 ± 1.35	0.03 ± 0.01	0.24 ± 0.06	0.031	0.001
expl3	DDB0169422	0.74 ± 0.08	0.40 ± 0.08	0.35 ± 0.06	0.14 ± 0.03	0.00 ± 0.00	0.00 ± 0.00	7.2E-10	0.001
guaA	DDB0215334	0.94 ± 0.06	4.70 ± 0.50	0.22 ± 0.03	0.41 ± 0.07	0.24 ± 0.08	0.80 ± 0.13	2.6E-05	4.5E-04
idhB	DDB0231294	0.62 ± 0.08	0.49 ± 0.06	2.89 ± 0.66	0.18 ± 0.03	0.61 ± 0.10	0.55 ± 0.28	0.087	0.011
N/A	DDB0204602	0.52 ± 0.10	0.10 ± 0.02	172 ± 170	1.82 ± 0.53	0.10 ± 0.02	119 ± 118	0.602	0.811

N/A, no name assigned to this gene.

*The data are averages and standard errors of two independent experiments, each done in triplicate.

^†From an ANOVA, considering genotype, treatment, and replication as parameters. Genotype and treatment are shown; the P values for treatments were all >0.05 (data not shown), indicating that biological and technical replications did not contribute significantly to the fold change.

Table 4. Distribution of cisplatin response genes in transcriptional modes

Mode*	Cisplatin response genes	Total genes in mode	Expected^†	c²	P value
1	41	191	18.437	27.613	1.48E-07
2	6	44	4.247	0.723	0.395
3	86	664	64.094	7.487	0.006
4	26	298	28.765	0.266	0.606
5	57	461	44.499	3.512	0.061
6	36	492	47.492	2.781	0.095
7	20	199	19.209	0.033	0.857
8	54	553	53.380	0.007	0.932
9	1	22	2.124	0.595	0.441
10	2	11	1.062	0.829	0.363
11	4	66	6.371	0.882	0.348
12	19	201	19.402	0.008	0.927
13	6	123	11.873	2.905	0.088
14	0	28	2.703	2.703	0.100
15	43	553	53.380	2.018	0.155
16	2	20	1.931	0.002	0.960
17	64	912	88.033	6.561	0.010
Total	467	4,838

*Modes are defined as groups of coregulated genes that are developmentally coregulated in wild type and in several mutant strains under various conditions as described in ref. 1.

^†467 ´ (total genes in mode)/4838.

1. Booth EO, Van Driessche N, Zhuchenko O, Kuspa A, Shaulsky G (2005) Bioinformatics 21:4371-4377.