Supplementary File 3. RIP-Chip identification of mRNAs preferentially associated with BAP-Msi1. We list all mRNAs that were determined to be enriched in the BAP-MSI1 associated population in relation to both BAP-GFP and BAP-PABP1 by using LIMMA model. Three fold enrichment in Msi1 array signal compared to controls and a spot intensity equal or higher than the average microarray spot intensity were established as threshold for target identification. Adjusted P-values were calculated for all the selected genes based on the LIMMA model used.

Symbol / Enrichment over BAP-GFP / Adjusted P Value / Symbol / Enrichment over BAP-PABP1 / Adjusted P Value
AASDHPPT / 3.2 / 2.06E-08 / AASDHPPT / 3.25 / 8.83E-08
ACTR2 / 3.16 / 1.74E-08 / ACTR2 / 3.82 / 7.03E-07
AMD1 / 4.03 / 3.61E-08 / AMD1 / 3.09 / 9.46E-08
ANKRD46 / 3.15 / 6.50E-09 / ANKRD46 / 3.37 / 2.82E-07
ARL6IP1 / 5.07 / 7.32E-09 / ARL6IP1 / 8.2 / 5.61E-08
ARL6IP5 / 3.52 / 5.48E-09 / ARL6IP5 / 3.1 / 1.02E-07
ATP6AP2 / 3.03 / 7.80E-08 / ATP6AP2 / 3.49 / 2.48E-07
ATP6V1G1 / 4.98 / 3.78E-08 / ATP6V1G1 / 4.12 / 1.28E-07
BTG3 / 3.25 / 1.31E-07 / BTG3 / 5.96 / 8.87E-07
C20orf30 / 5.64 / 9.94E-08 / C20orf30 / 5.15 / 5.61E-08
C4orf46 / 3.4 / 1.89E-07 / C4orf46 / 3.35 / 1.91E-07
C5orf15 / 3.33 / 1.28E-08 / C5orf15 / 4.38 / 2.28E-06
CCNG2 / 3.32 / 2.18E-08 / CCNG2 / 3.06 / 5.61E-08
CD164 / 4.22 / 8.11E-09 / CD164 / 3.97 / 2.04E-07
CDKN2A / 3.15 / 6.22E-09 / CDKN2A / 3.11 / 2.34E-07
CKAP2L / 4.26 / 1.51E-07 / CKAP2L / 3.24 / 5.63E-08
DEPDC1 / 3.48 / 1.23E-07 / DEPDC1 / 3.41 / 9.46E-08
DHRS2 / 4.63 / 5.91E-09 / DHRS2 / 8.09 / 5.61E-08
DHRS2 / 3.9 / 8.11E-09 / DHRS2 / 6.69 / 1.41E-07
ELOVL5 / 3.16 / 1.07E-08 / ELOVL5 / 3.16 / 1.60E-07
ERH / 3.59 / 7.32E-09 / ERH / 3.23 / 1.13E-07
FAM76B / 3.02 / 2.41E-08 / FAM76B / 3.74 / 2.11E-07
FBXO28 / 4.21 / 6.05E-09 / FBXO28 / 4.64 / 1.02E-07
GPR137B / 3.63 / 2.22E-08 / GPR137B / 4.4 / 1.01E-07
GRPEL2 / 3.23 / 3.04E-08 / GRPEL2 / 3.61 / 2.51E-06
H1F0 / 3.18 / 7.32E-09 / H1F0 / 3.11 / 1.02E-06
HERPUD1 / 3.13 / 6.54E-08 / HERPUD1 / 7.46 / 1.23E-07
HIGD1A / 3.6 / 6.85E-09 / HIGD1A / 3.47 / 8.11E-08
HIST2H4B / 3.23 / 1.08E-07 / HIST2H4B / 3.15 / 5.02E-07
HSBP1 / 3.84 / 1.44E-08 / HSBP1 / 3.59 / 1.47E-07
HSD17B6 / 3.45 / 5.91E-09 / HSD17B6 / 4.68 / 9.41E-08
KIAA0101 / 6.96 / 1.00E-08 / KIAA0101 / 3.4 / 5.61E-08
LBR / 3.22 / 1.07E-08 / LBR / 6.11 / 2.34E-07
OSAP / 3.17 / 1.16E-08 / OSAP / 3.09 / 1.73E-07
OSTM1 / 3.02 / 1.16E-08 / OSTM1 / 6.28 / 3.35E-07
PIGF / 4.4 / 8.85E-09 / PIGF / 3.37 / 5.61E-08
PKNOX1 / 3.41 / 8.11E-09 / PKNOX1 / 3.86 / 3.72E-07
PMAIP1 / 3.82 / 3.31E-08 / PMAIP1 / 3.52 / 1.83E-07
PMAIP1 / 3.8 / 2.07E-08 / PMAIP1 / 3.65 / 1.32E-07
PMAIP1 / 3.8 / 4.63E-08 / PMAIP1 / 3.55 / 9.91E-08
PMAIP1 / 3.77 / 1.98E-08 / PMAIP1 / 3.57 / 5.61E-08
PMAIP1 / 3.72 / 2.67E-08 / PMAIP1 / 3.64 / 1.96E-07
PMAIP1 / 3.72 / 4.20E-08 / PMAIP1 / 3.55 / 2.34E-07
PMAIP1 / 3.71 / 2.82E-08 / PMAIP1 / 3.6 / 1.05E-07
PMAIP1 / 3.7 / 2.00E-08 / PMAIP1 / 3.53 / 5.61E-08
PMAIP1 / 3.67 / 7.37E-09 / PMAIP1 / 3.27 / 5.61E-08
PMAIP1 / 3.53 / 3.34E-08 / PMAIP1 / 3.23 / 1.49E-07
PSPH / 3.55 / 6.22E-09 / PSPH / 3.13 / 6.62E-08
PTBP2 / 3.47 / 8.77E-09 / PTBP2 / 3.61 / 1.83E-07
PTP4A1 / 3.15 / 1.09E-08 / PTP4A1 / 5.04 / 2.19E-07
RAB11A / 3.35 / 8.37E-09 / RAB11A / 5.15 / 1.94E-07
RABGGTB / 3.09 / 1.79E-08 / RABGGTB / 4.06 / 4.26E-07
RCN2 / 4.35 / 2.67E-08 / RCN2 / 6.23 / 5.61E-08
RNF11 / 3.09 / 2.34E-08 / RNF11 / 5.3 / 4.24E-07
RNF138 / 3.2 / 3.76E-08 / RNF138 / 3.97 / 2.07E-07
RNF146 / 3.05 / 6.27E-08 / RNF146 / 3.58 / 1.18E-07
SCML1 / 3.67 / 1.27E-08 / SCML1 / 4.02 / 1.66E-07
SGPP1 / 3.05 / 3.65E-08 / SGPP1 / 4.46 / 1.38E-07
SLC16A1 / 3.13 / 3.39E-08 / SLC16A1 / 4.26 / 2.44E-06
SNX10 / 3.26 / 1.07E-08 / SNX10 / 4.72 / 1.72E-07
SPCS2 / 4.08 / 2.22E-08 / SPCS2 / 5.37 / 5.61E-08
SRP14 / 4.36 / 1.16E-08 / SRP14 / 3.14 / 6.35E-08
STMN1 / 3.76 / 5.48E-09 / STMN1 / 4.18 / 6.13E-08
TCEA1 / 3.13 / 2.20E-08 / TCEA1 / 4.31 / 1.69E-06
TIGD2 / 3.14 / 6.50E-09 / TIGD2 / 3.02 / 2.91E-07
TMCO1 / 6.26 / 5.16E-09 / TMCO1 / 4.55 / 5.61E-08
TMEM165 / 3.57 / 5.91E-09 / TMEM165 / 3.27 / 8.83E-08
TMEM188 / 3.38 / 6.18E-09 / TMEM188 / 3.16 / 1.94E-07
TMEM209 / 3.36 / 1.11E-08 / TMEM209 / 3.5 / 2.00E-07
TOMM20 / 3.07 / 1.03E-08 / TOMM20 / 3.87 / 1.34E-07
TSNAX / 3.63 / 5.02E-08 / TSNAX / 3.19 / 1.68E-07
TSPAN3 / 3 / 1.68E-08 / TSPAN3 / 5.81 / 2.36E-07
UBE2E3 / 5.68 / 8.37E-06 / UBE2E3 / 3.78 / 1.09E-06
WTAP / 3.48 / 6.50E-09 / WTAP / 3.52 / 2.72E-07