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.