Columbia University: Computational Human High-grade Glioblastoma Multiforme Interactome - miRNA (Post-transcriptional) Layer
The Human High-Grade Glioma Interactome (HGi) contains a genome-wide complement of molecular interactions that are Glioblastoma Multiforme (GBM)-specific. HGi v3 contains the post-transcriptional layer of the HGi, which includes the miRNA-target (RNA-RNA) layer of the interactome.
microRNA target predictions were obtained using a two-step machine learning approach. First, sites predicted using miRanda, PITA and TargetScan were scored by classifying sites against a gold standard of validated interactions using a Support Vector Machine (SVM). The SVM is trained on features including the normalized score from the predicting algorithm, conservation across mammalian genomes, and site location relative to the start and end positions of the 3’ UTR. Then co-expression, site scores, and modular site grammar were used to predict interactions with SVM. Features and parameters were selected using cross validation and produced high confidence predictions after retraining the SVM on the complete dataset.
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For questions, please contact Kenneth Smith.