FIG 3.

Proteins identified via affinity purification followed by mass spectrometry (AP-MS) analysis of nuclear protein lysates acquired from huT-78 cells transduced with FLAG-tagged BCL11B or the N-terminal domain. (A) AP-MS data from discovery experiments (DDA) was used to identify high-confidence interacting proteins by combined stringent filters of a log₂ ratio of 2 (in comparison with mock) and a WD score of 1. BCL11B and NuRD components are in red and other proteins in gray. (B) The list of candidate confidently copurified proteins with the corresponding baits was submitted and visualized using the PINA4MS application in Cytoscape. PINA4MS uses an existing ensemble of protein-protein interaction databases to connect two proteins, thereby establishing a network. Coloring is according the bait used. (C) Relative quantitative values in comparison with mock obtained from discovery experiments using log₂ ratio-based relative coloring of BCL11B and the proteins belonging to the NuRD complex that were copurified, along with the corresponding baits.