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Fig. 5 | BMC Bioinformatics

Fig. 5

From: A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers

Fig. 5

Selected candidate elements in the three studied genomes. a Graphical legend for sequence features present in panel B and C. FIMO hits for position-specific weight matrices (PSWMs) are reported as 3′-pointing arrows. Occurrences for matrices 1 to 3 are labeled as “FIMO hit for element signatures (early)”, while those for PSWMs 4 and 5 are named “FIMO hit for element signatures (late)”; hits for matrices 6 and 7 are indicated as “FIMO hit for element signatures (J)”. Finally, occurrences for single transcription factor binding sites are called “FIMO hit for HD binding sites” (for homeodomain sites, PSWM 8) and “FIMO hit for O/E binding sites” (for olfactory/early B sites, PSWMs 9 to 12). We named “Novel candidate element” any region (derived from conservation tracks and used for FIMO searches) yielding FIMO hits for two rounds of PSWM alignment. “Novel candidate element (BLAST-derived)” sequences are produced by a pipeline variant, which requires conserved stretches to contain a core 13-bp motif prior to undergo FIMO analyses. b DNA maps for ten selected predicted elements (extended 2 Kb upstream and downstream) in mouse (GRCm38), rat (Rnor_6.0) and human (GRCh38). Each putative enhancer region (genomic coordinates on the left) is reported as a black thin arrow encompassing the whole page width. On it, annotations are found. Each FIMO hit comes with a number (corresponding to the PSWM associated to it), a significance level (* for q < 0.05; ** for q < 0.01; *** for q < 0.001) and one or more capital letters. These indicate the list(s) in which the candidate element was found; for mouse, 1 Mb threshold: A, T-cell receptor (TCR) genes; B, main olfactory epithelium (MOE), BLAST-derived pipeline variant; C, MOE; D, MOE (pseudogene-flagged genes pruned); E, vomeronasal organ (VNO); F, VNO (pseudogene-flagged genes pruned); G, olfactome; H, olfactome (pseudogene-flagged genes pruned); for rat and human, respectively (also 1 Mb threshold): I, olfactome; L, olfactome. FIMO hits resulting from a first-round PSWM alignment are represented above the element on which they are found; those yielded by second-round FIMO analyses are depicted below (second-round occurrences identical to first-round ones are systematically present but not reported). Within each round, when significance level varies between lists asterisk number conforms to its maximal value. c Sfaktiria is independently found by our framework, and it is duplicated in the rat. Maps are rendered as in panel B. Dashed shadowed boxes on mouse Sfaktiria highlight features deriving from the aforementioned pipeline variant, including first- and second-round FIMO hits; these comprise PSWM (1, 2, 6, 8) occurrences that do not contain information originating from Sfaktiria itself. Sfaktiria has two nearly identical counterparts in rat (at least in Rnor_6.0), pointed by gray-bordered shadowed arrows on the left

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