Table 3 Most abundant up-regulated functions
From: Cholesterol depletion induces transcriptional changes during skeletal muscle differentiation
COG level 2 | COG level 3 | COG function | Control relative frequency (%) | MbCD relative frequency (%) | Corrected p-values | Effect size | 95.0% lower CI | 95.0% upper CI |
|---|---|---|---|---|---|---|---|---|
Cell communication | Adherens junction | Lim domain only protein 7 | 0 | 0.036 | 3.37E-55 | -0.040 | -0.041 | -0.030 |
Cell growth and death | Apoptosis | cAMP-dependent protein kinase regulator | 0 | 0.028 | 4.69E-43 | -0.028 | -0.032 | -0.023 |
Transport and catabolism | Lysosome | Lysosomal-associated membrane protein 1/2 | 0 | 0.025 | 4.35E-39 | -0.025 | -0.030 | -0.021 |
Cell growth and death | p53 signaling pathway | Cytochrome c | 0 | 0.023 | 3.30E-36 | -0.023 | -0.028 | -0.019 |
Cell growth and death | p53 signaling pathway | BH3 interacting domain death agonist | 0 | 0.021 | 1.01E-32 | -0.021 | -0.025 | -0.017 |
Transport and catabolism | Lysosome | CD63 antigen | 0 | 0.021 | 1.82E-32 | -0.021 | -0.025 | -0.017 |
Cell growth and death | Cell cycle | Regulatory protein SWI5 | 0 | 0.021 | 3.25E-32 | -0.021 | -0.025 | -0.017 |
Cell growth and death | Oocyte meiosis | Aurora kinase A | 0 | 0.020 | 6.84E-31 | -0.020 | -0.024 | -0.016 |
Transport and catabolism | Lysosome | AP-3 complex subunit delta-1 | 0 | 0.019 | 1.69E-29 | -0.019 | -0.023 | -0.015 |
Cell communication | Focal adhesion | Classical protein kinase C | 0 | 0.019 | 9.94E-29 | -0.019 | -0.022 | -0.015 |
Transport and catabolism | Endocytosis | Hepatocyte growth factor-regulated tyrosine kinase | 0 | 0.018 | 3.59E-27 | -0.018 | -0.021 | -0.014 |
Transport and catabolism | Regulation of autophagy | Autophagy-related protein 4 | 0 | 0.017 | 1.24E-26 | -0.017 | -0.021 | -0.014 |
Transport and catabolism | Phagosome | Vesicle transport protein SEC22 | 0 | 0.017 | 1.58E-25 | -0.017 | -0.020 | -0.013 |
Cell motility | Regulation of actin cytoskeleton | Bradykinin receptor B2 | 0 | 0.017 | 1.57E-25 | -0.017 | -0.020 | -0.013 |
Transport and catabolism | Endocytosis | Vacuolar protein sorting-associated protein 45 | 0 | 0.015 | 1.10E-23 | -0.015 | -0.018 | -0.012 |
Transport and catabolism | Lysosome | AP-1 complex subunit sigma 1/2 | 0 | 0.014 | 1.47E-21 | -0.014 | -0.017 | -0.011 |
Transport and catabolism | Endocytosis | ESCRT-I complex subunit MVB12 | 0 | 0.014 | 9.84E-21 | -0.014 | -0.017 | -0.010 |
Cell growth and death | Cell cycle | ATP-dependent Lon protease | 0 | 0.012 | 7.22E-18 | -0.012 | -0.015 | -0.009 |
Cell communication | Focal adhesion | p21-activated kinase 1 | 0 | 0.011 | 2.45E-17 | -0.012 | -0.011 | -0.008 |
Cell communication | Adherens junction | Snail 2 | 0 | 0.011 | 2.43E-17 | -0.012 | -0.011 | -0.008 |
Transport and catabolism | Endocytosis | E3 ubiquitin-protein ligase NRDP1 | 0 | 0.011 | 3.15E-16 | -0.011 | -0.014 | -0.008 |
Cell communication | Focal adhesion | Calpain-2 | 0 | 0.011 | 5.87E-16 | -0.011 | -0.014 | -0.008 |