Table 2 Most abundant down-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 growth and death | Apoptosis | Interleukin-1 receptor-associated kinase 2 | 0.012 | 0.000 | 5.30E-20 | 0.012 | 0.008 | 0.015 |
Cell communication | Focal adhesion | Platelet derived growth factor C/D | 0.040 | 0.016 | 7.68E-14 | 0.024 | 0.018 | 0.031 |
Transport and catabolism | Phagosome | Rab-interacting lysosomal protein | 0.008 | 0.000 | 1.73E-13 | 0.008 | 0.005 | 0.011 |
Cell communication | Tight junction | GTPase KRas | 0.008 | 0.000 | 1.73E-13 | 0.008 | 0.005 | 0.011 |
Cell growth and death | Cell cycle | Growth arrest and DNA damage-inducible protein | 0.062 | 0.035 | 2.54E-09 | 0.027 | 0.018 | 0.035 |
Cell growth and death | Cell cycle | Regulator of sigma E protease | 0.108 | 0.072 | 3.14E-09 | 0.036 | 0.024 | 0.048 |
Cell growth and death | Cell cycle | Proliferating cell nuclear antigen | 0.115 | 0.080 | 4.06E-08 | 0.035 | 0.023 | 0.047 |
Transport and catabolism | Lysosome | AP-4 complex subunit mu-1 | 0.005 | 0.000 | 8.67E-08 | 0.005 | 0.002 | 0.007 |
Cell growth and death | Meiosis | Meiosis induction protein kinase IME2/SME1 | 0.004 | 0.000 | 1.91E-07 | 0.004 | 0.002 | 0.007 |
Cell growth and death | Cell cycle | RAD24; cell cycle checkpoint protein | 0.004 | 0.000 | 4.09E-07 | 0.004 | 0.002 | 0.006 |
Cell communication | Adherens junction | Sorbin and SH3 domain containing 1 | 0.004 | 0.000 | 4.08E-07 | 0.004 | 0.002 | 0.006 |
Cell communication | Focal adhesion | Fast skeletal myosin light chain 2 | 0.420 | 0.356 | 5.04E-07 | 0.064 | 0.041 | 0.088 |
Transport and catabolism | Lysosome | cathepsin A (carboxypeptidase C) | 0.032 | 0.016 | 5.05E-07 | 0.016 | 0.010 | 0.022 |
Cell communication | Tight junction | Myosin heavy chain | 1.108 | 1.002 | 5.82E-07 | 0.105 | 0.067 | 0.144 |
Cell growth and death | Cell cycle | Cyclin-dependent kinase inhibitor 1A | 0.039 | 0.022 | 1.43E-06 | 0.017 | 0.010 | 0.024 |
Transport and catabolism | Lysosome | Arylsulfatase B | 0.004 | 0.000 | 1.90E-06 | 0.004 | 0.002 | 0.006 |
Cell growth and death | Cell cycle | Cyclin E | 0.003 | 0.000 | 8.83E-06 | 0.003 | 0.001 | 0.005 |
Cell communication | Focal adhesion | Actinin alpha | 0.363 | 0.309 | 9.84E-06 | 0.053 | 0.031 | 0.075 |
Cell growth and death | Cell cycle | Cell cycle sensor histidine kinase DivJ | 0.015 | 0.006 | 1.30E-05 | 0.009 | 0.005 | 0.013 |
Cell communication | Gap junction | Cyclin-dependent kinase 1 | 0.048 | 0.030 | 2.08E-05 | 0.018 | 0.010 | 0.025 |