Table 2. Proteins elevated on chromatin in the absence of APC, but with unchanged dynamics of chromatin association.

name	ID	description	max pept Nr	fc up	fc up set 1	fc up set 2	P
MGC69154	148225843	hypothetical protein LOC379587	4, 8/1, 3	3.02	1.24	10.46	1.00
pcbp2	147901405	poly(rC) binding protein 2	7, 5/1, 4	2.02	1.20	3.80	0.62
eif3h	148225274	eukaryotic translation initiationfactor 3 subunit H	2, 3/2, 1	1.90	1.50	3.34	0.84
zhx3	148233976	zinc fingers and homeoboxes 3	14, 26/1, 2	1.79	1.37	3.41	1.00
txndc9	27924448	Apacd-prov protein	1, 2/3, 4	1.74	1.91	1.60	0.89
bub3	147900009	budding uninhibited bybenzimidazoles 3 homolog	2, 5/2, 2	1.64	1.66	1.41	0.88
mcts1-a	148236942	malignant T cell-amplified sequence1-A	3, 3/9, 11	1.54	1.52	1.95	0.75

The total amount of the signal for each protein ID in control or APC-depleted sample was calculated as a sum of the values in all time points from the smoothened profile, and averaged between the two sets. These values were further normalized to the total signal from all protein IDs in either control or APC-depleted samples in this dataset. The fold change increase (“fc up”) was calculated as a ratio between APC-depleted and control total values calculated as above. For individual sets, the fold change increase (“fc up set 1” and “fc up set 2”) was calculated from the raw data (not smoothened and not normalized to the total signal in the whole sample). Only data with a reproducible increase in the total signal in the absence of APC are presented. The positive Pearson coefficient (P) (P>0.3) given in the last row confirms similarity in dynamics of these proteins between APC-deficient and control samples. The maximum number of peptides detected in mock-depleted extract (set I), APC-depleted extract (set I)/mock-depleted extract (set II), APC-depleted extract (set II) are provided.