The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without an a priori binary classification of genes as targets or non-targets. When compared to other TF mining resources, MAGIC displayed favourable performance in predicting TFs and cofactors that drive gene changes in 4 settings:
1) A cell line expressing or lacking single TF,
2) Breast tumors divided along PAM50 designations
3) Whole brain samples from WT mice or mice lacking a single TF in a particular neuronal subtype
4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels.
In summary, MAGIC is a standalone application that produces meaningful predictions of TFs and cofactors in transcriptomic experiments.
More at https://uwmadison.app.box.com/s/8j90e5h2rjrsz3bacaxnq8kor2o64vyg
