Transcription factor binding motifs

MeinteR identifies putative binding sites of: (a) conserved transcription factors in human/mouse/rat alignments and (b) human transcription factors included in the JASPAR’s core collection (version 2018)⁶⁶. Conserved factors and their ~5.8 million genome-wide binding loci are retrieved from the corresponding track of the UCSC Table Browser. The intersection of the binding loci and the genomic coordinates of the regions flanking each DMS is exported and comparatively visualized against the expected frequency. For the detection of JASPAR’s profile matrices, MeinteR uses the scanning algorithm implemented in TFBSTools⁶⁷, in order to identify high-scoring matches between transcription factor profile matrices and DMS in user-defined sequence offset. To speed-up the analysis of large datasets, searches can be narrowed-down to promoters or CpG islands. In addition, MeinteR allows users to select a list of transcription factors, among hundreds available, and perform targeted enrichment analyses, excluding the “noisy” binding sites.