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Figure 2 | BMC Bioinformatics

Figure 2

From: MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model

Figure 2

Output of "Transcription Factor regulation". (A) Result of the query predicting TFs which potentially regulate the miR-200 family (cluster of down-regulated hsa-mir-200a, hsa-mir-200b, hsa-mir-429 represented here as down-regulated, green color code) with stringent criteria: quality score ≥ 0.85, number of miRNA by TF ≥ 3, and Fisher test p-value ≤ 0.05. The four predicted TFs are shown. Results are sorted by the quality score (lower panel). Information on all TF scores, including targeted miRNAs and the number of potential TFBS in a frame are given (shown only for ZEB2). All results, including generated graphs, can be visualized, memorized and exported in various formats. (B) Generated regulation graph with all input miRNAs shown here as down-regulated (diamonds in green) and predicted TFs (squares in gray). Edges represent regulations, and the gray canonical color code corresponds to the quality score. (C) Detail result interface showing the hsa-mir-200b upstream sequence (black line) with all TFBS (black boxes) predicted for ZEB2 and predicted promoter sequences (yellow or orange bar below the black line). A table ranks TFBS by quality score, and includes: "ID" (corresponding to the position in the sequence), sequence size, binding sequence, quality score, localization (within the upstream sequence and the genome through a hypertext link), and potential localization within a predicted promoter (orange boxes).

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