Affinity Comparator

macbook with slider image 3The Affinity Comparator is designed to graphically compare the specificity of different proteins within or between protein families. The goal is to provide biologists with an easy-to-use interface to perform detailed studies of the subtle differences in specificity between homologous transcription factors (TFs) and RNA-binding proteins (RBPs). TFs and RBPs within the same family typically bind to similar sequences. Genomes have evolved to capitalize on these small intrafamily specificity differences so that those factors can effectively regulate different downstream target genes. We created the Affinity Comparator to both quantify and graphically depict these differences in specificity. The currently available plots include:

1. 2-D Affinity Scatter Plot between a primary affinity model on the y-axis and multiple secondary models on the x-axis

  • Supports zoom, pan, and reset
  • Supports both linear and log scales
  • Supports Affinity models of different lengths
  • Calculates Pearson correlations between the primary model and all the secondary models

2. 3-D Affinity Scatter Plot between three affinity models

  • Supports zoom, pan, rotation, and reset
  • K-mers can be labeled by an affinity threshold
  • Supports projection onto all 3 axes
  • Easily re-assign proteins to different axes

3. Differential Sequence Energy Landscape (Di-SEL) Surface & Curtain Plots between two affinity models

  • Visualizes the affinity fold-change space between two TFs or RBPs as the highest-affinity sequence undergoes an increasing number of point mutations. Coloring of the surface or curtains helps to reveal any nucleotide affinity biases in the sequence-space.
  • Supports zoom, pan, rotation, and reset
  • Supports both 3D surface and curtains plots
  • K-mers can be labeled by an affinity fold-change threshold
  • Supports projection onto 2 axes
  • Supports log scale
  • Supports coloring by nucleotide content
  • Max number of point mutations is configurable

4. Affinity Change Tetrahedron Plots between two affinity models

  • Plots the specificity difference at each position in the binding site within a 3-dimensional tetrahedron. Each corner of the tetrahedron depicts complete specificity for 1 of the 4 DNA or RNA nucleotides.
  • Supports zoom, pan, rotation, and reset
  • Specificity points are colored by binding site position
  • Supports projection onto all 3 axes
  • Star plot measures the magnitude of specificity