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| Symbol | Gene name | GenBank accession no. | Function |
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| Apoptosis |
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| BAX | BCL2-associated X | NM_001291428
NM_001291429
NM_001291430
NM_001291431
NM_004324
NM_138761
NM_138763
NM_138764 | This gene encodes a mitochondrially localized protein with conserved B-cell lymphoma 2 homology motifs. Overexpression of the encoded protein induces apoptosis. |
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| CASP3 | Caspase 3, apoptosis-related cysteine peptidase | NM_004346
NM_032991 | Encodes protein as a cysteine-aspartic acid protease that plays a central role in the execution-phase of cell apoptosis. |
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| CASP7 | Caspase 7, apoptosis-related cysteine peptidase | NM_145248
XM_006725153
XM_006725154
XM_005268295
XM_006725155
XM_005268294
XM_006719962 | This gene encodes a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. |
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| CASP9 | Caspase 9, apoptosis-related cysteine peptidase | NM_001229
NM_032996 | Encodes a member of the cysteine-aspartic acid protease (caspase) family, which is involved in the execution-phase of cell apoptosis. |
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| Autophagy |
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| ATG5 | Autophagy-related 5 | NM_001286106.1
NM_001286107.1
NM_001286108.1
NM_001286111.1
NM_004849.4 | The protein encoded by this gene, in combination with autophagy protein 12 functions as an E1-like activating enzyme in a ubiquitin-like conjugating system. The encoded protein is involved in several cellular processes, including autophagic vesicle formation, mitochondrial quality control after oxidative damage, negative regulation of the innate antiviral immune response, lymphocyte development and proliferation, MHC II antigen presentation, adipocyte differentiation, and apoptosis. Several transcript variants encoding different protein isoforms have been found for this gene. |
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| ATG12 | Autophagy-related 12 | NM_001277783.2
NM_004707.4 | Autophagy is a process of bulk protein degradation in which cytoplasmic components, including organelles, are enclosed in double-membrane structures called autophagosomes and delivered to lysosomes or vacuoles for degradation. ATG12 is the human homolog of a yeast protein involved in autophagy. |
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| LAMP2 | Lysosomal-associated membrane protein 2 | NM_001122606.1
NM_002294.3
NM_013995.2 | The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. |
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| LC3B | Microtubule-associated protein 1 light chain 3 beta | NM_022818.5 | The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component. |
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| PARK2 | Parkin RBR E3 ubiquitin protein ligase | NM_004562.3
NM_013987.3
NM_013988.3 | The precise function of this gene is unknown; however, the encoded protein is a component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrate proteins for proteasomal degradation. Mutations in this gene are known to cause Parkinson disease and autosomal recessive juvenile Parkinson disease. Alternative splicing of this gene produces multiple transcript variants encoding distinct isoforms. Additional splice variants of this gene have been described but currently lack transcript support. |
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| ER stress |
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| DDIT3 | DNA damage inducible transcript 3 | NM_001195053.1
NM_001195054.1
NM_001195055.1
NM_001195056.1
NM_001195057.1
NM_004083.5 | This gene encodes a member of the CCAAT/enhancer-binding protein (C/EBP) family of transcription factors. The protein functions as a dominant-negative inhibitor by forming heterodimers with other C/EBP members, such as C/EBP and LAP (liver activator protein) and preventing their DNA binding activity. The protein is implicated in adipogenesis and erythropoiesis, is activated by endoplasmic reticulum stress, and promotes apoptosis. Fusion of this gene and FUS on chromosome 16 or EWSR1 on chromosome 22 induced by translocation generates chimeric proteins in myxoid liposarcomas or Ewing sarcoma. Multiple alternatively spliced transcript variants encoding two isoforms with different length have been identified. |
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| XBP1 | X-box binding protein 1 | NM_001079539.1
NM_005080.3 | This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. It may increase expression of viral proteins by acting as the DNA binding partner of a viral transactivator. It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). The resulting loss of 26 nt from the spliced mRNA causes a frame-shift and an isoform XBP1(S), which is the functionally active transcription factor. The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. A pseudogene of XBP1 has been identified and localized to chromosome 5. |
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| Antioxidant |
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| GPX3 | Glutathione peroxidase 3 | NM_002084 | The protein encoded by this gene belongs to the glutathione peroxidase family, members of which catalyze the reduction of organic hydroperoxides and hydrogen peroxide (H2O2) by glutathione, and thereby protects cells against oxidative damage. Several isozymes of this gene family exist in vertebrates, which vary in cellular location and substrate specificity. |
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| SOD2 | Superoxide dismutase 2 | NM_000636 | This gene is a member of the iron/manganese superoxide dismutase family. It encodes a mitochondrial protein that forms a homotetramer and binds one manganese ion per subunit. This protein binds to the superoxide byproducts of oxidative phosphorylation and converts them to hydrogen peroxide and diatomic oxygen. |
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| NQO1 | NAD(P)H quinone dehydrogenase 1 | NM_000903.3
NM_001025433.2
NM_001025434.2
NM_001286137.2 | This gene is a member of the NAD(P)H dehydrogenase (quinone) family and encodes a cytoplasmic 2-electron reductase. This FAD-binding protein forms homodimers and reduces quinones to hydroquinones. This protein’s enzymatic activity prevents the one electron reduction of quinones that results in the production of radical species. Mutations in this gene have been associated with tardive dyskinesia (TD), an increased risk of hematotoxicity after exposure to benzene, and susceptibility to various forms of cancer. Altered expression of this protein has been seen in many tumors and is also associated with Alzheimer’s disease (AD). Alternate transcriptional splice variants, encoding different isoforms, have been characterized. |
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| Mitochondrial replication |
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| POLG | DNA polymerase gamma, catalytic subunit | NM_001126131.2 | This gene encodes the catalytic subunit of mitochondrial DNA polymerase. Defects in this gene alter the replication of mitochondrial DNA and may cause progressive external ophthalmoplegia with mitochondrial DNA deletions 1 (PEOA1), among other diseases. |
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| POLRMT | RNA polymerase mitochondrial | NM_005035.4 | The polypeptide encoded by this gene is a mitochondrial DNA-directed RNA polymerase. The role of the gene product is mitochondrial gene expression and providing RNA primers to initiate replication of the mitochondrial genome. |
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| TFAM | Transcription factor A, mitochondrial | NM_001270782.1 | This gene encodes an important mitochondrial transcription factor. This encoded protein also plays a role in mitochondrial DNA replication and repair. Alzheimer’s and Parkinson’s diseases have been associated with sequence polymorphisms in this gene. |
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| Glial marker |
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| GFAP | Glial fibrillary acidic protein | NM_001131019.3 | The protein encoded by this gene is a major intermediate filament protein of mature astrocytes. This protein is utilized as a marker during development to distinguish astrocytes from the other glial cells. Gene mutations cause a disorder called Alexander disease, which affects astrocytes in the central nervous system. The result of alternative splicing is distinct isoforms encoded by multiple transcript variants. |
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| Neuronal marker |
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| MAP2 | Microtubule-associated protein 2 | NM_001039538.2 | The protein encoded by this gene belongs to the family of microtubule-associated proteins. Proteins in this family are involved in microtubule assembly, an essential step in neurogenesis. Similar genes in rat and mouse encode neuron-specific cytoskeletal proteins in dendrites, suggesting a role in determining dendritic shape during the development of the neuron. Several distinct isoforms encoded by alternatively spliced variants have also been described. |
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| Neuroprotective factors |
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| MDK | Midkine | NM_001012333.2 | The protein encoded by this gene is part of the small family of secreted growth factors that has the ability to bind heparin and respond to retinoic acid. This encoded protein functions to promote cell growth, migration, and angiogenesis, which is most prominent during tumorigenesis. This gene has been studied as a therapeutic target in a variety of disorders. Multiple isoforms encoded by alternatively spliced transcript variants have been described. |
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| PTN | Pleiotrophin | NM_001321386.2 | This gene encodes a secreted heparin-binding growth factor. The encoded protein functions in cell growth and survival and migration, as well as angiogenesis and tumorigenesis. Multiple transcript variants result from alternative splicing and alternative promoters. |
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| FGF2 | Fibroblast growth factor 2 | NM_001361665.2 | This gene encodes a protein that is part of the family of fibroblast growth factors (FGF). Members of the FGF family bind heparin and function in broad mitogenic and angiogenic activities. The gene product has been implicated in a diverse array of biological processes, including development of the limbs and nervous system, tumor growth, and wound healing. The mRNA of this gene has multiple polyadenylation sites and results in five different isoforms due to alternative translation from non-AUG (CUG) and AUG initiation codons. The isoforms initiated by CUG are localized in the nucleus and play a role in the intracrine effect, whereas the form initiated by AUG is typically in the cytosol and plays a role in this FGF’s paracrine and autocrine effects. |
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| Housekeeping gene |
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| HMBS | Hydroxymethylbilane synthase | NM_000190.4 | The protein encoded by this gene is part of the hydroxymethylbilane synthase superfamily. The gene product is the third enzyme in the heme biosynthetic pathway and serves as a catalyst for the head to tail condensation of four molecules of porphobilinogen into the linear hydroxymethylbilane. Gene mutations are linked to the autosomal dominant disease acute intermittent porphyria. |
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| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | NM_001256799.3 | The protein encoded by this gene is part of the glyceraldehyde-3-phosphate dehydrogenase family. The gene product catalyzes an important step in the metabolism of carbohydrates, the oxidative phosphorylation of glyceraldehyde-3-phosphate when in the presence of both nicotinamide adenine dinucleotide (NAD) and inorganic phosphate. |
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| MT-ND2 | Mitochondrially encoded NADH dehydrogenase 2 | NC_012920.1 | The gene product is a core subunit of the NADH dehydrogenase complex in the mitochondrial membrane respiratory chain. This complex plays a role in the electron transfer from NADH to the respiratory chain. Ubiquinone is believed to be the immediate electron acceptor for this enzyme. Diseases in association with this gene include Leber optic atrophy. |
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| RNA18SN5 | RNA, 18S ribosomal N5 | NR_003286.4 | The 45S ribosomal DNA (rDNA) clusters are designated as RNR1 through RNR5 on chromosomes 13, 14, 15, 21, and 22, respectively. The 445S rDNA has a repeat unit encoding a 45S rRNA precursor that gets processed to produce the 18S, 5.8S, and 28S rRNAs. As such, this gene is a representative copy of 18S rRNA, whose chromosomal location is not known. |
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