Table 2 TFs for which the binding to the Alu-associated BM has been experimentally verified. Most passed T1 and FDR of 20%. The last two (marked by **) did not pass our promoter regions search, but were reported in the literature as bound to Alu. Four TFs (bold) are new: they were found by us but their being bound to Alu went unnoticed. The first column is the PSSM symbol from MatInspector [30] or TRANSCFAC [31] the second and third columns are the gene symbol and description of the biological process. The last two columns list those target genes of each TF that have on-Alu BSs, and the appropriate references.

V$PITX2_Q2

PITX2

Eye, heart, tooth and abdominal organs

PLOD1

[40,42]

V$NKX25.01

Nkx2.5

Heart formation

PLOD1

[42]

V$LYF1.01*

ZNFN1A1 (LYF1)

T-cell differentiation

CD8

[27]

V$GFI1.01

Gfi-1

Hematopoietic differentiation

AZU, P21, JAK3, ACT, AAT

[41]

V$LXRE.01*

LXREα

[56]

V$ER.01–02

ER

BRCA1, ERF-3

[18]

V$RAR.01*

RARA

Retonic acid receptors family. Embryonic morphogenesis

Keratin K18

[22]

V$GC.01*

SP1

Nuclear factor. Tumer suppressor

[21]

V$LUN1

LUN1

Lung development

[39]

V$PAX6.02**

PAX6**

Pancreas development

[45]

V$YY1.01**

YY1**

Nuclear factor

[20]