Genes Related to Mitochondrial Functions, Protein Degradation, and Chromatin Folding Are Differentially Expressed in Lymphomonocytes of Rett Syndrome Patients

Table 4

GO analysis of genes reported to be deregulated in PBMC of RTT patients.

Term	Description	𝑃 value	Fold enrichment
Cluster 1
GO:0022900	Electron transport chain	2.0×10^−12	9.01
GO:0006091	Generation of precursor metabolites and energy	1.7×10^−12	5.06
GO:0045333	Cellular respiration	2.7×10^−12	9.71
GO:0006120	Mitochondrial electron transport, NADH to ubiquinone	4.9×10^−12	16.32
GO:0022904	Respiratory electron transport chain	1.8×10^−11	12.04
GO:0006119	Oxidative phosphorylation	2.0×10^−11	9.17
GO:0042775	Mitochondrial ATP synthesis coupled electron transport	2.0×10^−11	12.99
GO:0042773	ATP synthesis coupled electron transport	2.0×10^−11	12.99
GO:0015980	Energy derivation by oxidation of organic compounds	3.4×10^−9	6.54
GO:0055114	Oxidation reduction	1.5×10^−8	3.01
Cluster 2
GO:0006626	Protein targeting to mitochondrion	4.3×10^−3	8.81
GO:0070585	Protein localization in mitochondrion	4.3×10^−3	8.81
GO:0045039	Protein import into mitochondrial inner membrane	7.5×10^−3	28.54
GO:0007007	Inner mitochondrial membrane organization	2.8×10^−2	19.03
GO:0006839	Mitochondrial transport	3.1×10^−2	4.96
Cluster 3
GO:0051436	Negative regulation of ubiquitin-protein ligase activity during mitotic cell cycle	1.8×10^−4	7.24
GO:0051444	Negative regulation of ubiquitin-protein ligase activity	2.1×10^−4	7.03
GO:0051352	Negative regulation of ligase activity	2.1×10^−4	7.03
GO:0051437	Positive regulation of ubiquitin-protein ligase activity during mitotic cell cycle	2.4×10^−4	6.92
GO:0051443	Positive regulation of ubiquitin-protein ligase activity	2.8×10^−4	6.73
GO:0051439	Regulation of ubiquitin-protein ligase activity during mitotic cell cycle	3.0×10^−4	6.63
GO:0051351	Positive regulation of ligase activity	3.7×10^−4	6.45
GO:0051438	Regulation of ubiquitin-protein ligase activity	6.2×10^−4	6.04
GO:0051340	Regulation of ligase activity	8.4×10^−4	5.81
GO:0043086	Negative regulation of catalytic activity	8.4×10^−3	2.78
GO:0044092	Negative regulation of molecular function	9.6×10^−3	2.56
Cluster 4
GO:0031145	Anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process	1.8×10^−4	7.24
GO:0010498	Proteasomal protein catabolic process	4.4×10^−3	4.62
GO:0043161	Proteasomal ubiquitin-dependent protein catabolic process	4.4×10^−3	4.62
Cluster 5
GO:0031397	Negative regulation of protein ubiquitination	4.1×10^−4	6.36
GO:0031400	Negative regulation of protein modification process	9.2×10^−4	4.68
GO:0031398	Positive regulation of protein ubiquitination	1.0×10^−3	5.61
GO:0032269	Negative regulation of cellular protein metabolic process	3.2×10^−3	3.58
GO:0031396	Regulation of protein ubiquitination	4.2×10^−3	4.71
GO:0051248	Negative regulation of protein metabolic process	4.4×10^−3	3.43
GO:0031401	Positive regulation of protein modification process	4.1×10^−2	2.98
GO:0032268	Regulation of cellular protein metabolic process	4.7×10^−2	2.08
Cluster 6
GO:0065003	Macromolecular complex assembly	1.4×10^−8	2.96
GO:0043933	Macromolecular complex subunit organization	9.9×10^−8	2.77
GO:0034622	Cellular macromolecular complex assembly	3.2×10^−6	3.63
GO:0034621	Cellular macromolecular complex subunit organization	2.6×10^−5	3.24
GO:0065004	Protein-DNA complex assembly	1.1×10^−4	6.12
GO:0034728	Nucleosome organization	5.2×10^−4	5.52
GO:0006461	Protein complex assembly	2.1×10^−3	2.37
GO:0070271	Protein complex biogenesis	2.1×10^−3	2.37
Cluster 7
GO:0006334	Nucleosome assembly	2.4×10^−4	6.12
GO:0031497	Chromatin assembly	3.1×10^−4	5.90
GO:0006323	DNA packaging	8.2×10^−4	4.76
GO:0006333	Chromatin assembly or disassembly	6.0×10^−3	4.04
Cluster 8
GO:0008380	RNA splicing	5.6×10^−6	3.77
GO:0006396	RNA processing	5.7×10^−6	2.82
GO:0006397	mRNA processing	1.5×10^−4	3.20
GO:0000398	Nuclear mRNA splicing, via spliceosome	2.0×10^−4	4.48
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	2.0×10^−4	4.48
GO:0000375	RNA splicing, via transesterification reactions	2.0×10^−4	4.48
GO:0016071	mRNA metabolic process	8.5×10^−4	2.78
Cluster 9
GO:0006412	Translation	2.6×10^−8	4.01
GO:0006414	Translational elongation	5.4×10^−5	5.93
Cluster 10
GO:0006367	Transcription initiation from RNA polymerase II promoter	1.1×10^−3	6.30
GO:0006352	Transcription initiation	4.5×10^−3	5.16
Cluster 11
GO:0006368	RNA elongation from RNA polymerase II promoter	1.1×10^−3	7.13
GO:0006354	RNA elongation	4.5×10^−3	6.71