Table 3 Functional categories of proteins differentially expressed in MDA-MB-231-ShB cells compared to MDA-MB-231-ShNC cells

Apoptosis [n = 7, 8%]

BAX (1.50, 4.53E-02), FADD (1.63, 2.17E-02), DIO-1 (25.39, 5.91E-55), AKAP95 (2.19, 4.12E-06), PGRMC1 (0.62, 0.01), GNAS (0.53, 3.30E-4), TFG (0.59, 6.19E-03)

DNA repair and cell cycle [n = 8, 9%]

SMC1A (1.62, 4.66E-02), ANAPC10 (0.11, 4.30E-44), PPP1CB (0.64, 3.35E-2), PPP2R1A (0.46, 4.1E-06), CRABP2 (4.24, 5.69E-20), C10orf78 (2.21, 3.14E-06), NXN (0.60, 0.01), TK1 (0.61, 8.50E-03)

Gene regulation, RNA expression, mRNA splicing, and protein synthesis and transport [n = 30, 33%]

RBBP4 (1.68, 2.18E-02), WDR5 (8.98, 2.37E-24), ZNF259 (1.52, 4.84E-02), SFRS5 (1.60, 2.16E-02), STAU1 (1.63, 1.30E-02), RPL37A (1.53, 0.04), EIF2S2 (1.57, 0.03), TMED2 (1.56, 2.98E-02), KIAA0521 (1.77, 2.00E-03), SRP14 (2.28, 3.14E-05), HNRPA1L-2 (7.61, 7.77E-38), SRP72 (0.26, 2.07E-17), RGPD5 (0.36, 5.44E-10), PQBP1 (0.44, 2.57E-06), TERF2IP (0.47, 8.95E-06), SEC23B (0.49, 4.08E-05), SUPT5H (0.51, 1.78E-04), FUBP1 (0.52, 2.79E-04), PPP1R14B (0.52, 2.79E04), CPSF3 (0.57, 2.75E-03), HMGA1 (0.58, 5.70E-03), RPS15 (0.60, 6.49E-03), KIAA1150 (0.60, 2.75E-03), ELAC2 (0.61, 9.85E-03), FARSA (0.62, 0.01), SNRNP70 (0.63, 0.02), BASP1 (0.64, 0.03), KIAA0324 (0.65, 0.04), PRPF4 (0.65, 0.48), MAGED2 (0.65, 0.02)

Metabolism [n = 11, 12%]

ATP5C1 (1.62, 0.02), PGLS (0.59, 4.34E-03), PGAM4 (0.38, 6.95E-10), ACAA1 (0.03, 6.80E-104), ACOT2 (0.37, 8.07E-10), USMG5 (1.55, 3.69E-02), GCDH (1.69, 5.90E-03), ALDH9A1 (6,60, 5.67E-33), RRM2 (0.47, 1.18E-06), AK1 (0.49, 1.44E-10), VAT1 (0.57, 3.66E-03)

Cytoskeleton, cell adhesion and cell motility [n = 14, 15%]

S100A11 (1.82, 1.13E-03), TACC3 (0.58, 4.54E-03), WASL (0.10, 3.76E-48), PPP1R9B (0.25, 1.40E-18), TNXB (0.09, 2.43E-52), SEPT9 (0.57, 1.76E-03), NCKIPSD (1.54, 3.95E-02), ACTR3 (11.59, 1.39E-51), LUM (0.07, 7.40E-59), KIAA0345 (0.23, 6.31E20), THBS1 (0.41, 5.28E-09), ARHGEF2 (0.43, 8.89E-07), ZYX (0.43, 1E-06), SDCBP (0.53, 5.15E-04)

Ubiquitin proteasome pathway [n = 6, 7%]

UBE2V1 (0.63, 2.59E-02), ZFP91 (0.53, 3.87E-04), UBE2C (0.49, 3.04E-05), UBE2L3 (0.55, 3.88E-04), UBE2K (0.56, 1.61E-03), KIAA0439 (0.65, 0.03)

Oxidative Stress [n = 1, 1%]

DJ-1 (2.01, 7.10E-04)

Others [n = 14, 15%]

ACP1 (1.52, 4.72E-02), CYR61 (1.56, 3.49E-02), HBA1 (0.02, 7.30E-102), LTF (0.02, 3.80E-102), HBE1 (0.11, 2.89E-42), ALB (0.13, 2.21E-38), CHCHD2 (0.37, 3.94E-10), C19orf43 (0.39, 6,69E-09), CCDC86 (0.40, 4.27E-08), COX17 (0.45, 5.23E-06), C1orf122 (0.46, 6.59E-06), ZC3H18 (0.46, 8.95E-06), TXLNA (0.49, 9.02E-06), C11orf84 (0.52, 3.18E-05)