Research Article

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

Table 2

Genes upregulated in RTT patients by LIMMA and SAM analyses.

NCBI reference sequenceGene symbolGene nameMolecular functionBiological processFold change

NM_004541.3NDUFA1NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5 kDaNADH dehydrogenase (ubiquinone) activityMitochondrial electron transport, NADH to ubiquinone3.1

NM_006498.2LGALS2Lectin, galactoside-binding, soluble, 2Carbohydrate binding2.8

NM_014302.3SEC61GSec61 gamma subunitProtein transporter activityProtein targeting to ER; antigen processing and presentation of exogenous peptide antigen via MHC class I2.8

NM_001040437.1C6orf48Chromosome 6 open reading frame 482.7

NM_001098577.2RPL31Ribosomal protein L31RNA binding; structural constituent of ribosomeTranslational elongation; translational initiation; translational termination2.7

NM_006989.5RASA4RAS p21 protein activator 4GTPase activator activity; phospholipid bindingIntracellular signal transduction; positive regulation of GTPase activity; regulation of small GTPase mediated signal transduction2.6

NM_000983.3RPL22Ribosomal protein L22RNA binding; heparin binding; structural constituent of ribosomeAlpha-beta T cell differentiation; translational elongation; translational initiation; translational termination2.6

NM_019059.3TOMM7Translocase of outer mitochondrial membrane 7 homolog (yeast)Protein transmembrane transporter activityCellular protein metabolic process; protein import into mitochondrial matrix; protein targeting to mitochondrion2.6

NM_031157.2HNRNPA1Heterogeneous nuclear ribonucleoprotein A1Nucleotide binding; single-stranded DNA binding; single-stranded RNA bindingRNA export from nucleus; mRNA splicing, via spliceosome; mRNA transport; nuclear import2.5

NM_001828.5CLCCharcot-Leyden crystal galectinCarbohydrate binding; carboxylesterase activity; lysophospholipase activityLipid catabolic process; multicellular organismal development2.4

NM_032901.3COX14Cytochrome c oxidase assembly homolog 14 (S. cerevisiae)Plays a role in the assembly or stability of the cytochrome c oxidase complex (COX)Mitochondrial respiratory chain complex IV assembly2.3

NM_024960.4PANK2Pantothenate kinase 2ATP binding; pantothenate kinase activityCell death; coenzyme A biosynthetic process; coenzyme biosynthetic process; pantothenate metabolic process2.3

NR_002309.1RPS26P11Ribosomal protein S26 pseudogene 11Structural constituent of ribosomeTranslation2.3

NM_005003.2NDUFAB1NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8 kDaNADH dehydrogenase (ubiquinone) activity; ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process; fatty acid binding; calcium ion bindingCellular metabolic process; protein lipoylation; small molecule metabolic process; respiratory electron transport chain; fatty acid biosynthetic process; mitochondrial electron transport, NADH to ubiquinone2.3

NM_152851.2MS4A6AMembrane-spanning 4-domains, subfamily A, member 6AMay be involved in signal transduction as a component of a multimeric receptor complex2.3

NM_004269.3MED27Mediator complex subunit 27Transcription coactivator activityRegulation of transcription from RNA polymerase II promoter; stem cell maintenance; transcription initiation from RNA polymerase II promoter2.2

NR_015404.1C12orf47MAPKAPK5 antisense RNA 12.2

NM_001865.3COX7A2Cytochrome c oxidase subunit VIIa polypeptide 2 (liver)Cytochrome-c oxidase activity; electron carrier activityOxidative phosphorylation2.2

NM_004374.3COX6CCytochrome c oxidase subunit VIcCytochrome-c oxidase activityRespiratory electron transport chain; small molecule metabolic process2.2

NM_002984.2CCL4Chemokine (C-C motif) ligand 4Chemokine activityCell adhesion; cell-cell signaling; chemotaxis; immune response; inflammatory response; positive regulation of calcium ion transport; positive regulation of calcium-mediated signaling; positive regulation of natural killer cell chemotaxis;
response to toxic substance; response to virus; signal transduction
2.2

NM_014060.2MCTS1Malignant T cell amplified sequence 1RNA bindingCell cycle; positive regulation of cell proliferation; regulation of growth; regulation of transcription, DNA-dependent; response to DNA damage stimulus transcription, DNA-dependent2.1

NM_004832.2GSTO1Glutathione S-transferase omega 1Glutathione dehydrogenase (ascorbate) activity; glutathione transferase activity; methylarsonate reductase activityL-ascorbic acid metabolic process; glutathione derivative biosynthetic process; negative regulation of ryanodine-sensitive calcium-release channel activity; positive regulation of ryanodine-sensitive calcium-release channel activity; positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion; regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion; xenobiotic catabolic process2.1

NM_001867.2COX7CCytochrome c oxidase subunit VIIcCytochrome-c oxidase activityRespiratory electron transport chain; small molecule metabolic process2.1

NM_014206.3C11orf10Transmembrane protein 2582.1

NM_002413.4MGST2Microsomal glutathione S-transferase 2Enzyme activator activity; glutathione peroxidase activity; glutathione transferase activity; leukotriene-C4 synthase activityGlutathione biosynthetic process; glutathione derivative biosynthetic process; leukotriene biosynthetic process; positive regulation of catalytic activity; xenobiotic metabolic process2.1

NM_001124767.1C3orf78Small integral membrane protein 42.1

NM_152398.2OCIAD2OCIA domain containing 22.1

NM_002488.4NDUFA2NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8 kDaNADH dehydrogenase (ubiquinone) activityMitochondrial electron transport, NADH to ubiquinone small molecule metabolic process2.1

NM_004528.3MGST3Microsomal glutathione S-transferase 3Glutathione peroxidase activity;
glutathione transferase activity
Glutathione derivative biosynthetic process; lipid metabolic process; signal transduction; small molecule metabolic process
xenobiotic metabolic process
2.0

NM_003095.2SNRPFSmall nuclear ribonucleoprotein polypeptide FRNA bindingHistone mRNA metabolic process; mRNA 3′-end processing
ncRNA metabolic process; spliceosomal snRNP assembly; termination of RNA polymerase II transcription
2.0

NM_005213.3CSTACystatin A (stefin A)Cysteine-type endopeptidase inhibitor activity; protein binding, bridging
structural molecule activity
Cell-cell adhesion; keratinocyte differentiation; peptide cross-linking2.0

NM_033318.4C22orf32Single-pass membrane protein with aspartate-rich tail 12.0

NM_053035.2MRPS33Mitochondrial ribosomal protein S33Structural constituent of ribosomeTranslation2.0

BC014670.1LOC147727Hypothetical protein LOC147727, mRNA (cDNA clone IMAGE: 4864993), partial cds2.0

NM_001014.4RPS10Ribosomal protein S10Protein bindingTranslational elongation; translational initiation; translational termination; viral transcription2.0

NM_001130710.1LSM5LSM5 homolog, associated U6 small nuclear RNA (S. cerevisiae)RNA bindingRNA splicing; exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;
mRNA processing
2.0

NM_002801.3PSMB10Proteasome (prosome, macropain) subunit, beta type, 10Threonine-type endopeptidase activityDNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; G1/S transition of mitotic cell cycle; T cell proliferation; anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process; apoptotic process; cell morphogenesis; gene expression; humoral immune response; mRNA metabolic process; negative regulation of apoptotic process; negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; protein polyubiquitination; regulation of cellular amino acid metabolic process; small molecule metabolic process2.0

NM_014044.5UNC50Unc-50 homolog (C. elegans)RNA bindingCell surface receptor signaling pathway; protein transport2.0

NM_032747.3USMG5Up-regulated during skeletal muscle growth 5 homolog (mouse)Plays a critical role in maintaining the ATP synthase population in mitochondria2.0

NM_001001330.2REEP3Receptor accessory protein 3May enhance the cell surface expression of odorant receptors2.0

NM_004074.2COX8ACytochrome c oxidase subunit VIIIA (ubiquitous)Cytochrome-c oxidase activityRespiratory electron transport chain; small molecule metabolic process2.0

NM_002493.4NDUFB6NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17 kDaNADH dehydrogenase (ubiquinone) activityMitochondrial electron transport, NADH to ubiquinone; small molecule metabolic process2.0

NM_032273.3TMEM126ATransmembrane protein 126AOptic nerve development2.0

“—”: lacking item.