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. 2016 Aug 26;90(18):8059–8073. doi: 10.1128/JVI.00553-16

TABLE 2.

HIV-1 integration site preference in PHA-activated, TN, and TCM CD4+ T cells

Sample No. (%) of unique integration sites
 Avg gene density within 1 Mb (±0.5 Mb) of integration sitesa
Total Within RefSeq genes Within 5 kb (±2.5 kb) of a transcriptional start site Within 5 kb (±2.5 kb) of a CpG island
Activated CD4+ T cells 133,697 114,110 (85.3)c 6,242 (4.7)d 7,052 (5.3)e 20.3f
CD4+ TN cells 729 613 (84.1)g 30 (4.1%)h 33 (4.5)i 18.4j
CD4+ TCM cells 2,620 2,291 (87.4)k 109 (4.2%)l 112 (4.3)m 19.0n
MRCb 50,000 22,328 (44.7) 2,010 (4.0) 2,100 (4.2) 8.7
a

Based on complete genes.

b

Matched random control of 50,000 computer-generated integration sites in proximity to Mse1/BglII restriction sites in hg19.

c

P value (Fisher's exact test) versus values for the following: MRC, <2.2 × 10−308; TCM cells, 0.003; TN cells, 0.34.

d

P value (Fisher's exact test) versus values for the following: MRC, 1.7 × 10−9; TCM cells, 0.24; TN cells, 0.53.

e

P value (Fisher's exact test) versus values for the following: MRC, 1.0 × 10−21; TCM cells, 0.02; TN cells, 0.41.

f

P value (Wilcoxon rank-sum) versus values for the following: MRC, <2.2 × 10−308; TCM cells, 0.045; TN cells, 0.0002.

g

P value (Fisher's exact test) versus values for the following: MRC, 3.5 × 10−106; TCM cells, 0.02.

h

P value (Fisher's exact test) versus values for the following: MRC, 0.85; TCM cells, 1.

i

P value (Fisher's exact test) versus values for the following: MRC, 0.64; TCM cells, 0.76.

j

P value (Wilcoxon rank-sum) versus values for the following: MRC, 1.7 × 10−101; TCM cells, 0.017.

k

P value (Fisher's exact test) versus the value for the MRC, <2.2 × 10−308.

l

P value (Fisher's exact test) versus the value for the MRC, 0.72.

m

P value (Fisher's exact test) versus the value for the MRC, 0.84.

n

P value (Wilcoxon rank-sum) versus the value for the MRC, <2.2 × 10−308.