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

Table 3

Genes down-regulated in RTT patients by LIMMA and SAM analyses.

NCBI reference sequence	Gene symbol	Gene name	Molecular function	Biological process	Fold change
NM_170601.4	SIAE	Sialic acid acetylesterase	Sialate O-acetylesterase activity	—	−2.3
NR_002312.1	RPPH1	Ribonuclease P RNA component H1	—	—	−2.2
NM_005322.2	HIST1H1B	Histone cluster 1, H1b	DNA binding	Nucleosome assembly	−1.8
NM_000902.3	MME	Membrane metalloendopeptidase	Metalloendopeptidase activity	Proteolysis	−1.8
NM_032047.4	B3GNT5	UDP-GlcNAc: betaGal beta-1,3-N-acetylglucosaminyltransferase 5	Galactosyltransferase activity	Glycolipid biosynthetic process; posttranslational protein modification	−1.7
NM_003513.2	HIST1H2AB	Histone cluster 1, H2ab	DNA binding	Nucleosome assembly	−1.7
NR_002562.1	SNORD28	Small nucleolar RNA, C/D box 28	—	—	−1.5
NM_004668.2	MGAM	Maltase-glucoamylase (alpha-glucosidase)	Alpha-glucosidase activity; amylase activity	Carbohydrate metabolic process	−1.5
NM_012081.5	ELL2	Elongation factor, RNA polymerase II, 2	—	Regulation of transcription, DNA-dependent	−1.4
NM_021066.2	HIST1H2AJ	Histone cluster 1, H2aj	DNA binding	nucleosome assembly	−1.4
NM_002424.2	MMP8	Matrix metallopeptidase 8 (neutrophil collagenase)	Metalloendopeptidase activity; zinc ion binding	Proteolysis	−1.4
NM_004994.2	MMP9	Matrix metallopeptidase 9 (gelatinase B, 92 kDa, gelatinase, 92 kDa, type IV collagenase)	Collagen binding; metalloendopeptidase activity; zinc ion binding	Collagen catabolic process; extracellular matrix disassembly; positive regulation of apoptotic process; proteolysis	−1.4
NM_003533.2	HIST1H3I	Histone cluster 1, H3i	DNA binding	Nucleosome assembly; regulation of gene silencing	−1.3
NG_000861.4	GK3P	Glycerol kinase 3 pseudogene	ATP binding; glycerol kinase activity	Catabolic process; glycerol metabolic process	−1.3
NR_033423.1	LOC1720	Dihydrofolate reductase pseudogene	—	—	−1.3
NM_003521.2	HIST1H2BM	Histone cluster 1, H2bm	DNA binding	Nucleosome assembly	−13
NM_002417.4	MKI67	Antigen identified by monoclonal antibody Ki-67	ATP binding	DNA metabolic process; cell proliferation; cellular response to heat; meiosis; organ regeneration	−1.2
NM_020406.2	CD177	CD177 molecule	—	Blood coagulation; leukocyte migration	−1.2
NM_001039841.1	ARHGAP11B	Rho GTPase activating protein 11B	GTPase activator activity	Positive regulation of GTPase activity; regulation of small GTPase mediated signal transduction; small GTPase mediated signal transduction	−1.2
NM_001004690.1	OR2M5	Olfactory receptor, family 2, subfamily M, member 5	G-protein coupled receptor activity; olfactory receptor activity	Detection of chemical stimulus involved in sensory perception of smell	−1.2
NM_052966.3	FAM129A	Family with sequence similarity 129, member A	—	Negative regulation of protein phosphorylation; positive regulation of protein phosphorylation; positive regulation of translation; response to endoplasmic reticulum stress	−1.2
NM_001067.3	TOP2A	Topoisomerase (DNA) II alpha 170 kDa	ATP binding; DNA binding, bending; chromatin binding; drug binding; magnesium ion binding; ubiquitin binding	DNA ligation; DNA repair; DNA topological change; DNA-dependent DNA replication; apoptotic chromosome condensation; mitotic cell cycle; phosphatidylinositol-mediated signaling; positive regulation of apoptotic process; positive regulation of retroviral genome replication; positive regulation of transcription from RNA polymerase II promoter; sister chromatid segregation	−1.2
NM_021018.2	HIST1H3F	Histone cluster 1, H3f	DNA binding	S phase; blood coagulation; nucleosome assembly; regulation of gene silencing	−1.2
NM_182707.2	PSG8	Pregnancy specific beta-1-glycoprotein 8	The human pregnancy-specific glycoproteins (PSGs) are a group of molecules that are mainly produced by the placental; syncytiotrophoblasts during pregnancy. PSGs comprise a subgroup of the carcinoembryonic antigen (CEA) family, which; belongs to the immunoglobulin superfamily.	Female pregnancy	−1.2
NM_003535.2	HIST1H3J	Histone cluster 1, H3j	DNA binding	S phase; blood coagulation; nucleosome assembly; regulation of gene silencing	−1.2
NM_004566.3	PFKFB3	6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	6-Phosphofructo-2-kinase activity; ATP binding; fructose-2,6-bisphosphate 2-phosphatase activity	Fructose metabolic process; glycolysis; small molecule metabolic process	−1.2
NM_016448.2	DTL	Denticleless E3 ubiquitin-protein ligase homolog (Drosophila)	—	DNA replication; G2 DNA damage checkpoint; protein monoubiquitination; protein polyubiquitination; ubiquitin-dependent protein catabolic process	−1.2
NG_001019.5	IGHM	Immunoglobulin heavy constant mu	Antigen binding	Immune response	−1.2
NR_002907.2	SNORA73A	Small nucleolar RNA, H/ACA box 73A	—	—	−1.2

“—”: lacking item.