Inferring coregulation of transcription factors and microRNAs in breast cancer

Both transcription factors (TFs) and microRNAs (miRNAs) regulate gene expression. TFs activate or suppress the initiation of the transcription process and miRNAs regulate mRNAs post-transcriptionally, thus forming a temporally ordered regulatory event. Ectopic expression of key transcriptional regulators and/or miRNAs has been shown to be involved in various tumors. Therefore, uncovering the coregulation of TFs and miRNAs in human cancers may lead to the discovery of novel therapeutics.We introduced a two-stage learning fuzzy method to model TF–miRNA coregulation using both genomic data and verified regulatory relationships. In Stage 1, a learning (adaptive) fuzzy inference system (ANFIS) combines two sequence alignment features of TF and target by learning from verified TF–target pairs into a sequence matching score. Next, a non-learning FIS incorporates a sequence alignment score and a correlation score from paired TF–target gene expression to output a Stage 1 fuzzy score to infer whether a TF–target regulation exists. For significant TF–target pairs, in Stage 2, similar to Stage 1, we first infer whether a miRNA regulates each common target by an ANFIS, which incorporates their sequences and known miRNA–target relationships to output a sequence score. Next, an FIS incorporates the Stage 1 fuzzy score, Stage 2 sequence score and gene expression correlation score of a miRNA–target pair to determine whether TF–miRNA coregulation exists. We collected 54 (8) TF–miRNA–target triples validated in ER-positive (ER-negative) breast cancer cell lines in the same article, and they were used as positives. Negative examples were constructed for Stage 1 (Stage 2) by pairing TFs (miRNAs) with human housekeeping genes found in the literature; both positives and negatives were used to train ANFISs in the training step.This two-stage fizzy algorithm was applied to predict 54 (8) TF–miRNA coregulation triples in ER-positive (ER-negative) human breast cancer cell lines, and resulted in true-positive rates of 0.55 (0.74) and 0.57 (0.75) using 3-fold and n-fold cross validations (CVs), respectively. False-positive rate bound was 0.07 (0.13) for ER-positive (ER-negative) breast cancer using both 3-fold and n-fold CVs. Interestingly, among the 62 coregulatroy triples from ER-positive/negative breast cancer cells, about 72% have TF- and coregulatory miRNA expression simultaneously greater or less than the corresponding medians, while in the remaining 28% of TFs and their coregulatory miRNAs are conversely expressed. The proposed fuzzy algorithm performed well in identification of TF–miRNA coregulation triples in human breast cancer. After being trained by the corresponding verified coregulatory triples and genomic data, this algorithm can be applied to uncover novel coregulation in other cancers in the future.