Part C

• Restrict this to only DNA binding TFs (1639)

Figure 2

DONE Part D

How should I sort the GO terms? By number of significant conditions then P value?

• Yes, sort like this, but with shared at the top, every set moved to left
• Bigger circles

Figure 3

DONE Part A

Where does the HOMER_{TFdictionaryproper}.txt come from?

• Doesn't matter (this is just manual annotation)

Figure 4

• Only the ones that end in count (do a text search)
• No dendrograms
• Lupus should just be lupus (remove underscores)
• remove long disease

Figure 5

• Scatter plot between PU.1 MARIO ARS_GLOBAL and bQTL/AlphaGenome/SNPmoods
  • Ask Andrew/Xiaoting for:
    • Only PU.1 bound heterozygotes (hets)
    • All Mario Hets where there were at least 7 reads
    • UID/index, SNP ID (RSID), ARS_GLOBAL, DATASET, SNPmoods, bQTL (from bulyk lab's paper), ALphaGENOME (Andrew), Number of total Reads PU.1 to that SNP
  • Density scatter plot/heatmap?
  • Flow cytometry density plot is a good example