Fig. 2: QTG-Miner quickly narrows down candidate genes underlying 12 TBN QTLs in maize.
From: QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
a Multi-omics network map used by QTG-Miner. ChIA-PET, chromatin interaction analysis by paired-end tag sequencing. PPI, protein-protein interaction. b Positive and negative gene datasets used for the SD and ML algorithms. c Comparison of SD values from positive genes (n = 52), background genes (n = 26, 044) and negative genes (n = 62) to positive genes. The y-axis indicates the SD value. Violin plots: median ± upper and lower quartiles; P values were calculated from two-sided Student’s t tests. d AUC values obtained from five different ML algorithms. For five algorithms, n = 20 independent replicates, respectively. In each box plot, the center line indicates the median, the edges of the box represent the first and third quartiles, and the whiskers extend to span a 1.5 interquartile range from the edges. e Weighted SD value (SDw) of each gene in the candidate interval for 12 TBN QTLs. f Weighted probability (Pw) of each gene in 12 TBN QTLs, gray dotted line indicates the cutoff of machine learning. In e, f, Salmon solid dots indicate potential candidate genes, and gray solid dots indicate excluded genes.
