Gene networks and transcriptional regulators associated with liver cancer development and progression

Meier, Tatiana; Timm, Max; Montani, Matteo; Wilkens, Ludwig

doi:10.1186/s12920-021-00883-5

BMC Medical Genomics

Table 2 Chromosomal aberrations in hepatocellular carcinoma (HCC) subgroups with a low (GE1) and high (GE2) proliferation gene expression profile

From: Gene networks and transcriptional regulators associated with liver cancer development and progression

Chr	Arm	Type of aberration		Significant^a	HCC GE1		HCC GE2
Chr	Arm	GE1	GE2	Significant^a	Size^b of intervals	% cases affected	Size^b of intervals	% cases affected
1	p	Gain	–	Yes	175	50	116	8.3
1	p	Gain	Loss	No	885	30–50	885	33.3–41.7
1	q	Gain	Gain	No	2214	50–80	2214	41.7–83.3
2	p/q	Gain	Gain	No	92	50	92	33.3
3	p/q	Gain	Gain	No	195	50–70	252	33.3–66.7
4	q	–	Loss	Yes	0	0	783	41.7– 50.0
5	p	–	Loss	Yes	0	0	106	41.7
5	q	Gain	–	Yes	207	50	207	8.8
5	q	Gain	Loss	No	215	30–40	215	33.3
6	p	Gain	Gain	No	474	50–60	474	58.3–75
6	q	Gain	Loss	No	34	30	34	33.3
7	p/q	Gain	–	Yes	2111	40–70	915	8.3–25.0
7	q	Gain	Gain	Yes	34	90	34	41.7
7	p/q	Gain	Gain	No	298	60–90	298	33.3–58.3
8	p	Loss	Loss	No	286	30–50	286	58.3–75
8	p	Gain	Loss	No	55	30–50	28	41.7–50
8	q	Gain	Gain	No	1364	50–100	1364	33.3–66.7
9	p	Gain	Gain	No	34	50	34	33.3
9	q	Gain	Gain	No	292	80	292	50
10	q	Gain	Gain	No	16	60	16	41.7
11	p/q	Gain	Gain	No	169	60–80	169	41.7–50
11	q	Gain	Gain	Yes	400	100	400	50–58.3
12	p	Gain	–	Yes	85	60	85	16.7
12	q	Gain	Gain	Yes	188	80	188	33.3
12	p/q	Gain	Gain	No	213	50–80	213	33.3–50
13	q	–	Loss	Yes	568	10	1199	41.4–83.3
13	q	Gain	–	Yes	11	70	11	25
13	q	Gain	Gain	No	10	70	10	33,3
14	q	Gain	Gain	No	191	40–70	191	33.3–58.3
15	q	Gain	Gain	No	43	50	43	58.3
16	p/q	Gain	–	Yes	721	50–60	706	8.3–16.7
16	p	Gain	Gain	No	119	60	119	33.3–41.7
16	q	Gain	Loss	Yes/no	157	50	157	33.3–50
17	p	Gain	Loss	Yes/no	541	60–80	541	33.3–50
17	q	Gain	Gain	No	1452	40–50	1452	41.5–75
18	q	–	Loss	Yes	149	10	149	58.3
18	q	–	Loss	No^c	668	10	668	50
19	p	Gain	Gain	Yes	762	100	762	41.7–58.3
19	q	Gain	Gain	Yes	39	70–90	39	16.7–41.7
19	q	Gain	Gain	No	1030	80–90	1030	50
20	p/q	Gain	Gain	No	841	30–60	841	50–66.7
21	q	–	Loss	Yes	0	0	91	41,7
21	q	Gain	–	Yes	43	70	43	25
22	q	Gain	Gain	No	829	70–80	43	50

The table only includes aberrations that spanned more than 10 probes. Similar aberrations found in both HCC subgroups were included when they affected > 50% cases in one tissue set and > 30% cases in the other; they are presented in italics. Aberrations that presented changes in the opposite direction in the HCC subgroups were included when the aberration incidence in each subgroup was ≥ 30%
Chr chromosome
^aWe considered differential aberrations between the two HCC groups to be statistically significant when P < 0.05 in differential aberration analysis
^bThe interval size is expressed as the total number of probes that spanned the aberration interval
^cThe P value for differential loss of 18q in HCC-GE2 was 0.06

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