In parallel, we overlapped lncRNA-promoter-enriched TFBSs with ENCODE ChIP-seq experimental evidence for the corresponding TFs across all ENCODE ChIP-seq datasets [62]. A moderate FDR approach (Benjamini-Hochberg procedure) identified three TFs – GATA3, ARID3A, and MEF2A – as being dually supported by HOCOMOCO computational evidence of their TFBS overrepresentation at lncRNA promoters and by ENCODE ChIP-seq experimental evidence for their binding at lncRNA promoters genome-wide (Table S2). This intersection of TFBS overrepresentation at lncRNA promoters and empirical ChIP-seq support for the binding of these same TFs at those promoters provides important evidence that these three TFs may direct genome-wide lncRNA transcriptional programs in the ENCODE ChIP-seq-profiled cell types.
