Transcription factor binding site enrichment analysis

Over-represented transcription factor binding sites was performed on the 2kb region upstream from the transcriptional start site of all differentially expressed lncRNAs using the TRANSFAC^® database (www.biobase-international.com/transcription-factor-binding-sites from BIOBASE Corporation).²² The background sequences were randomly generated and default settings were used for all other parameters; the significance was set at a p-value < 0.01. Enrichment of E2F1 binding in HeLa-S3 cells was extracted from publically available peak calls through the ENCODE database.²³