Table 3.

Promoters overlapping repetitive elements

Location of differentially expressed repeat
Repeat overlapping promotersDifferentially expressed repeat overlapping promotersProtein coding
Repeat familyTotal# downOdds ratioP-value# upOdds ratioP-value5′UTRIntronExon3′UTRlncRNAPseudogeneNot annotated
REP522720012562.052.2E−1610009312
Low_complexity2,013132.374.7E−03181.040.8115226204
Simple_repeat11,982441.350.062042.132.2E−1686704717163
SINE/Alu3,961002.4E−051384.442.2E−165671111350
LINE/L13,42610.11.5E−03672.351.8E−092220012032
LINE/L23,22020.220.01250.90.724004017
LTR/ERVL-MaLR3,613007.8E−05310.991640010011
LTR/ERV13,93220.183.0E−031334.32.2E−167120031283
LTR/ERVL1,488000.04201.570.0492200808

NOTE: The table shows the numbers of upregulated and downregulated promoters that overlap nine families of repetitive elements (≥20 promoters) as well as Fisher exact statistics of the enrichments (odd ratios and P-value, two-sided test). The right side of the table shows the available information about the annotation of those promoters.