Table 1. Examples of significant associations of LINE, SINE, LTR and DNA transposons with genes that were previously linked to breast cancer as TEffectR outputs along with multiple covariates.

Expression levels of TEs within the upstream 5 kb regions of the given genes and other covariates such as the tissue type (healthy vs. tumor) or patient number were included in the linear regression model. The p-value of the model indicates the significance of the linear model. P-values for each covariate indicate whether these factors have significant associations with the expression of the given gene. Adjusted r-square score indicates the precision of the model with significant covariate associations in terms of predicting the expression of the gene. For example, an adjusted R square of 0.8422 indicates that the linear model could explain 84.22% of the gene’s expression.

Link to breast cancer	Gene name	TE name	r squared	Adjusted r-squared	Model p-value	Individual p-values
Biomarkera	KRT8 (CK8)	L2c (LINE)	0.8532	0.8422	1.026E–16	L2c: 1.356E–13 Tissue type: 0.0332 Patient: 0.7974
Prognosisb	SLC39A6 (LIV-1)	L2b (LINE)	0.7231	0.7023	3.100E–11	L2b: 7.536E–08 Tissue type: 0.0013 Patient: 0.1024
Molecular pathogenesisc	SAFB	L1MB7 (LINE)	0.5131	0.4766	2.107E–06	L1MB7: 1.114E–07 Tissue type: 0.6112 Patient: 0.1394
Susceptibilitydand prognosise	CHEK2	AluJb, AluSx AluS (SINE)	0.6362	0.5883	1.645E–07	AluJb: 0.0433 AluSx: 0.0426 AluSz: 0.0005 Tissue type: 0.0023 Patient: 0.0033
Susceptibilityfand prognosisg	FEN1	MIR3 (SINE)	0.5545	0.5211	3.703E–07	MIR3: 2.572E–06 Tissue type: 0.0122 Patient: 0.3886
Molecular genetics and pathogenesish	CENPL	AluSx3, AluY (SINE)	0.5489	0.5027	2.118E–06	AluSx3: 0.0007 AluY: 0.2000 Tissue type: 0.0066 Patient: 0.2467
Prognosisi	MCM4	MLT1D (LTR)	0.5733	0.5413	1.587E–07	MLT1D: 0.0012 Tissue type: 1.544E–06 Patient: 0.1674
Susceptibilityj	RMND1	LTR5_Hs (LTR)	0.4318	0.3892	4.279E–05	LTR5_Hs: 1.782E–05 Tissue type: 0.4280 Patient: 0.1193
Molecular pathogenesis and prognosisk	CPNE3	MLT1H2 (LTR)	0.3910	0.3453	0.0002	MLT1H2: 0.0002 Tissue type: 0.0055 Patient: 0.9407
Biomarker and prognosisl	HLA-DPB1	hAT-1_Mam (DNA)	0.8318	0.8192	1.548E–15	hAT-1_Mam: 1.092E–14 Tissue type: 0.5467 Patient: 0.2850
Molecular pathogenesismand biomarkern	HSPB2 (HSP27)	MER5B (DNA)	0.7756	0.7587	4.791E–13	MER5B: 8.050E–07 Tissue type: 0.5756 Patient: 0.1733
Molecular pathogenesiso	PARP9	MER5B (DNA)	0.5929	0.5624	6.287E–08	MER5B: 1.141E–06 Tissue type: 0.0054 Patient: 0.5464

Notes.

^aHeo et al. (2013).

^bKasper et al. (2005).

^cHammerich-Hille et al. (2010).

^dNagel et al. (2012)

^eLi et al. (2014); Li, Liang & Zhang (2014)

^fChung et al. (2015).

^gAbdel-Fatah et al. (2014).

^hTishchenko et al. (2016).

ⁱKwok et al. (2015).

^jDunning et al. (2016).

^kHeinrich et al. (2010).

^lForero et al. (2016).

^mWei et al. (2011).

ⁿStorm et al. (1995).

^oTang et al. (2018).