Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci -- Data Supplement - Supporting Tables -- Proceedings of the National Academy of Sciences

Supporting information for Zhang et al. (2003) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.2627983100

Table 11. Effect of boundary distance (d) on the analysis of chromosomal clustering of genes whose expression was altered in common between senescence and quiescence or specifically during quiescence in human fibroblasts

	No. of genes	Chr. distances	No. of clusters		P value	No. of clustered genes		P value
	No. of genes	Chr. distances	Observed	Expected	P value	Observed	Expected	P value
Proliferative arrest-associated up-regulation	246	1 kb	1	0.07	0.002	2	0.13	0.002
		2 kb	3	0.17	<0.001	6	0.34	<0.001
		5 kb	5	0.49	<0.001	10	0.98	<0.001
		10 kb	7	0.77	<0.001	14	1.53	<0.001
		20 kb	7	1.28	<0.001	14	2.56	<0.001
		50 kb	7	2.68	0.005	14	5.38	0.006
		100 kb	10	4.5	0.005	20	9.06	0.006
		200 kb	14	7.95	0.011	28	16.1	0.016
		500 kb	25	16.1	0.002	53	33.2	0.001
		1 Mb	42	25.6	<0.001	87	53.8	<0.001
		2 Mb	49	38.7	0.003	117	84.7	<0.001
		5 Mb	56	56.6	0.521	155	135.1	0.007
Quiescence specific up-regulation	282	1 kb	0	0.06	0.06	0	0.13	0.06
		2 kb	2	0.24	0.002	4	0.47	0.002
		5 kb	3	0.6	0.002	6	1.2	0.002
		10 kb	3	1.02	0.032	6	2.04	0.032
		20 kb	5	1.67	0.004	10	3.36	0.004
		50 kb	5	3.43	0.109	10	6.9	0.117
		100 kb	6	5.94	0.379	12	12	0.395
		200 kb	12	10.3	0.224	24	21	0.253
		500 kb	16	20.4	0.852	32	42.3	0.897
		1 Mb	28	32.6	0.833	58	69.1	0.88
		2 Mb	46	47.6	0.6	99	105.6	0.733
		5 Mb	69	67.5	0.311	165	165.5	0.499
Proliferative arrest-associated down-regulation	365	1 kb	0	0.2	0.144	0	0.3	0.144
		2 kb	1	0.4	0.07	2	0.9	0.07
		5 kb	1	1	0.286	2	2.1	0.287
		10 kb	1	1.8	0.543	3	3.6	0.543
		20 kb	4	2.8	0.138	9	5.7	0.138
		50 kb	10	5.8	0.034	21	11.7	0.034
		100 kb	16	9.8	0.016	33	19.8	0.016
		200 kb	26	16.7	0.006	54	34.1	0.004
		500 kb	38	32.5	0.098	81	68	0.086
		1 Mb	61	66.3	0.8	135	144.2	0.76
		2 Mb	86	92.8	0.895	202	213.9	0.825
		5 Mb	105	122.4	1	271	318.9	1
Quiescence specific down-regulation	250	1 kb	1	0.07	0.003	2	0.14	0.003
		2 kb	1	0.19	0.008	2	0.39	0.008
		5 kb	2	0.48	0.016	4	0.96	0.016
		10 kb	2	0.79	0.045	4	1.58	0.046
		20 kb	3	1.36	0.047	6	2.73	0.048
		50 kb	6	2.72	0.023	12	5.45	0.024
		100 kb	14	4.67	<0.001	28	9.42	<0.001
		200 kb	19	8.19	<0.001	38	16.6	<0.001
		500 kb	30	16.7	<0.001	63	34.3	<0.001
		1 Mb	35	26.3	0.014	78	55.4	0.006
		2 Mb	43	39.4	0.163	105	86.6	0.017
		5 Mb	54	57.8	0.792	150	138.6	0.085

A chromosomal cluster was defined as two or more genes located within the specified distance. Observed values indicate the number of chromosomal clusters identified by using the parameters shown and the number of genes present in those clusters. Expected values indicate the average number of false-positive clusters or false-positive clustered genes estimated by a bootstrapping algorithm as described in Materials and Methods. The P value indicates the probability that the difference between the observed and calculated incidence of clusters or clustered genes is due to random chance.