Johnson Lab: UCSF

(I recommend that you maximize these videos during playback.)

Demo#1: NEW PLOT menu and genome browser

This video shows the contents of the NEW PLOT configuration menu before and after a pre-configured plot settings file is loaded. The plot configuration is then opened in a plot tab and the video concludes with a demonstration of some of the interactive features of the plot. (Note that a legend can be toggled on/off… I forgot to include the legend in this demo.)

Demo#2: Three MochiView Utilities

This video shows a quick glimpse of utilities for identifying Motifs in a set of Locations ((Motif Finder (from Location), finding Motifs in the library that resemble a Motif (Motif Comparison), and comparing the Motif enrichment in different sets of Locations (Motif Score Plotter).

Demo#3: MANAGER menu

This video provides a quick tour of the MANAGER menu, where you can view/edit/delete the contents of the MochiView database.

Images from ‘Anchor plot’ utility

The images below (click to enlarge) were created using the ‘Utilities->Anchor plot‘ utility, and represent a summary of ChIP and motif data values and gene proximity relative to a set of anchor locations (ChIP peaks or promoters).

Screenshot: ‘Compact motif/data/location plot’ utility

The image below (click to enlarge) was created using the ‘Utilities->Compact motif/data/location‘ plot utility, and shows matches of the Zap1 motif to promoter sequences (with a ChIP data overlay).