TABLE 1.

Analysis of associations of chromosomal elements with breakpoints of unselected LOH events in furfural-treated cells^a

Chromosome element	Predicted no. of elements included in microarrays	No. observed		No. expected		P valueb
		Within tracts	Outside tracts	Within tracts	Outside tracts
tRNA genes	274	36	5,718	60	5,694	0.002
Autonomously replicating sequence elements	317	51	6,606	69	6,588	0.029
snRNA and snoRNA genes	83	19	1,724	18	1,725	0.830
Transposable elements	47	8	979	10	977	0.481
Solo LTRs	274	23	5,731	60	5,694	0.000
Centromeres	16	3	333	3	333	0.793
Palindromic sequences	570	125	11,845	124	11,846	0.947
G4 sequences	544	115	11,309	119	11,305	0.740
Highly transcribed genes	330	75	6,855	72	6,858	0.717
Weakly transcribed genes	312	56	6,496	68	6,484	0.143
Binding sites for Rrm3p	112	19	2,333	24	2,328	0.271
Regions with high levels of phosphorylated histone H2AX	631	135	13,116	138	13,113	0.826
Replication-termination sequences	71	17	1,474	15	1,476	0.697
Tandemly repeated sequences	1,125	277	23,348	245	23,380	0.042
Regions with high GC content (>42%)	538	215	11,083	117	11,181	0.000
Regions with low GC content (<36%)	407	49	8,498	89	8,458	0.000
Meiotic hot spots	136	37	2,819	30	2,826	0.175

^aThe table shows the expected numbers of elements within and outside LOH regions compared to the observed numbers of elements within and outside the regions (see Data Set S3). The chromosomal coordinates of chromosomal elements were provided by Song et al. (38).

^bThe two sets of data were compared using chi-square tests in Excel, and the resulting P values (for the differences between expected and observed values) are shown. The values in boldface were significant (P < 0.05) after correcting for multiple comparisons.