Table 2. List of specific genes for HAM/TSP.
DEGs up-regulated only in HAM/TSP.
| Gene Symbol | Product | Accession number | Gene ID |
Relative expression (fold change) |
Function and localization |
| MUC3A | mucin 3A, cell-surface associated | NM_005960 | 4584 | 40.6 | Unknown; O-glycosylation in S/T/P repeat |
| NAF1 | nuclear assembly factor 1 homolog (S. cerevisiae) | NM_138386 | 92345 | 13.7 | RNA binding, protein binding |
| ZC3H12D | Zinc finger CCCH-type containing 12D | NM_207360 | 340152 | 11.34 | Endonuclease activity; regulates macrophage |
| POFUT2 | Protein O-fucosyltransferase 2 isoform A | NM_015227 | 23275 | 10.71 | O-glycosylation in S/T residues in EGF or thrombospondin motifs |
| C14orf72 | Chromosome 14 open reading frame | XM_096733 | 145200 | 9.73 | hypothetical |
| CKS2 | CDC28 protein kinase regulatory subunit 2 | NM_001827 | 1164 | 9.13 | Cell cycle, cell proliferation, spindle organization |
| SMC4 | Structural maintenance of chromosome 4 | NM_005496 | 10051 | 7.38 | ATP, nucleotide, protein binding, cell cycle, division |
| SOX21 | SRY (sex determining region Y)-box 21 | NM_007084 | 11166 | 6.83 | transcription factor activity |
| KLHL21 | kelch-like protein 21 (Drosophila) | NM_014851 | 9903 | 6.81 | Protein binding |
| RABGAP1L | RAB GTPase activating protein 1-like isoform A | NM_014857 | 9910 | 6.71 | GTPase activator activity; intracellular |
| ATP1B1 | Na+/K+ -ATPase beta 1 subunit isoform a | NM_001677 | 481 | 6.68 | K ion binding; plasma membrane protein |
| WDR41 | WD repeat domain 41 | NM_018268 | 55255 | 6.49 | unknown |
| TDP1 | tyrosyl-DNA phosphodiesterase 1 | NM_018319 | 55775 | 6.39 | DNA repair, binding |
| BCL2L13 | BCL2-like protein 13 (apoptosis facilitator) | NM_015367 | 23786 | 6.30 | Caspase activator activity |
| RPS6KA5 | ribosomal protein S6 kinase, 90kDa, polypeptide 5 | NM_004755 | 9252 | 6.27 | ATP binding; cytoplasm, nucleus |
| MAML1 | Mastermind-like [domain containing] 1 | NM_005491 | 9794 | 5.95 | Regulation of transcription; nucleus |
| RABEP1 | rabaptin, RAB GTPase binding effector protein 1 isoform 1 | NM_004703 | 9135 | 5.54 | membrane fusion, GTPase activator activity; cytoplasm, endosome |
| IL-6ST | IL-6 signal transducer isoform 1 precursor (gp130, oncostatin M receptor) | NM_002184 | 3572 | 5.32 | IL-6, -11, -27 receptor activity; positive regulation of T cell proliferation; plasma membrane |
| TMEM39A | Transmembrane protein 9A | NM_018266 | 55254 | 5.2 | plasma membrane; transmembrane protein |
| S100P | S100 calcium binding protein P | NM_005980 | 6286 | 5.06 | Calcium and magnesium ion binding; cytoplasm, nucleus |
| AFF4 | AFF/FMR2 family, member 4 | NM_014423 | 27125 | 4.86 | Regulation of transcription; nucleus |
| SLFN5 | schlafen family, member 5 | NM_144975 | 162394 | 4.83 | ATP, nucleotide binding; cell differentiation; nucleus |
| SOD2 | Superoxide dismutase 2, mitochondrial | NM_000636 | 6648 | 4.83 | Magnesium ion binding; nucleus |
| RILPL2 | Rab interacting lysosomal protein-like 2 | NM_145058 | 196383 | 4.76 | Identical protein binding; cytoplasm, cytosol |
| PMFBP1 | Polyamine modulated factor 1 (PMF-1) binding protein 1 | NM_031293 | 83449 | 4.63 | Unknown; cytoplasm |
| RAN | Ras related nuclear protein | NM_006325 | 5901 | 4.50 | GTP binding, GTPase activity, mitotic spindle organization; cytosol, nucleus |
| PWP1 | PWP1 homolog (S. cerevisiae), endonuclein | NM_007062 | 11137 | 4.32 | Transcription; nucleus |
| MED28 | Mediator complex subunit 28 | NM_025205 | 80306 | 4.29 | actin binding, protein binding, regulation of transcription; cytoplasm, membrane, nucleus |
| HES2 | HES2 (hairy and enhancer of split 2 (Drosophila)) protein, hes family bHLH transcription factor 2 | NM_019089 | 54626 | 4.17 | DNA binding, transcription regulator activity; nucleus |
| FAM133B | family with sequence similarity 133, member B(hypothetical protein LOC257415) | NM_152789 | 257415 | 4.14 | Unknown |
| RRN3 | RNA polymerase I-specific transcription initiation factor RRN3 (TIF-IA) | NM_018427 | 54700 | 4.06 | Regulation of transcription; nucleoplasm, nucleus |
| HERPUD1 | homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 protein | NM_014685 | 9709 | 4.04 | protein binding, response to unfolded protein; ER |
| PRPS1L1 | phosphoribosyl pyrophosphate synthetase 1-like 1 | NM_175886 | 221823 | 3.86 | ATP, magnesium ion binding, kinase activity; cellular component |
| FBXO3 | F-box protein 3 | NM_012175 | 26273 | 3.81 | ubiquitin-protein ligase activity, proteolysis |
| PDCD2 | programmed cell death 2 isoform 1 | NM_002598 | 5134 | 3.75 | DNA, protein, zinc ion binding, apoptosis; cytoplasm, nucleus |
| SNAPC5 | small nuclear RNA activating complex, polypeptide 5, 19kDa subunit | NM_006049 | 10302 | 3.75 | Regulation of transcription; nucleus |
| BIRC3 | baculoviral IAP repeat-containing 3 (cIAP-2) | NM_001165 | 330 | 3.74 | ubiquitin-protein ligase activity, zinc ion binding, anti-apoptosis, signal transduction; cytoplasm, nucleus |
| ELN | elastin | NM_000501 | 2006 | 3.71 | extracellular matrix constituent; extracellular matrix |
| KRT1 | keratin 1 | NM_006121 | 3848 | 3.7 | Protein, sugar binding, receptor activity, cytoskeleton; plasma membrane |
| GALNT11 | UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11) | NM_022087 | 63917 | 3.69 | polypeptide N-acetylgalactosaminyltransferase activity; Golgi |
| IKZF5 | IKAROS family zinc finger protein 5 | NM_022466 | 64376 | 3.65 | DNA, zinc ion binding; intracellular, nucleus or NOT nucleus |
| TBC1D23 | TBC1 domain family, member 23 | NM_018309 | 55773 | 3.57 | Rab GTPase activator activity; intracellular |
| MRPL41 | mitochondrial ribosomal protein L41 | NM_032477 | 64975 | 3.52 | structural constituent of ribosome, apoptosis, cell cycle, translation; mitochondria, ribosome |
| NEUROG 3 | neurogenin 3 (class A basic helix-loop-helix protein 7) | NM_020999 | 50674 | 3.49 | Nervous system development, positive regulation of |
| CIRH1A | cirrhosis, autosomal recessive 1A (cirhin) | NM_032830 | 84916 | 3.49 | Molecular function; nucleolar, nucleus |
| NDUFB3 | NADH dehydrogenase (ubiquinone) 1 beta | NM_002491 | 4709 | 3.39 | NADH dehydrogenase (ubiquinone) activity, mitochondrial electron transport; mitochondria |
| PLA2G4D | phospholipase A2, group IVD (cytosolic) | NM_178034 | 283748 | 3.37 | calcium ion binding, hydrolase activity, phospholipase A2 activity; Cytosol, cytoplasm |
| PTBP1 | polypyrimidine tract binding protein 1 | NM_002819 | 5725 | 3.36 | RNA splicing; nucleolous, nucleoplasm, nucleus |
| HAND1 | heart and neural crest derivatives expressed 1, bHLHa27 | NM_004821 | 9421 | 3.34 | protein heterodimerization activity, transcription; nucleus |
| GMCL1 | germ cell-less homolog 1 (Drosophila) | NM_178439 | 64395 | 3.34 | protein binding, cell differentiation; nucleus |
| FAT2 | FAT tumor suppressor homolog 2 (Drosophila) | NM_001447 | 2196 | 3.29 | calcium ion, protein binding, cell adhesion; plasma membrane |
| WARS2 | tryptophanyl tRNA synthetase 2, mitochondrial | NM_201263 | 10352 | 3.29 | ATP, nucleotide binding, tryptophan-tRNA ligase activity; cytoplasm, mitochondria |
| CDX4 | caudal type homeobox transcription factor 4 | NM_005193 | 1046 | 3.29 | Sequence-specific DNA binding, transcription factor; nucleus |
| TDG | thymine-DNA glycosylase | NM_003211 | 6996 | 3.27 | DNA N-glycosylase activity, damaged DNA, mismatched DNA binding; nucleus |
| CCDC85C | coiled-coil domain containing [protein] 85C | NM_001144995 | 317762 | 3.27 | Unknown |
| ABL1 | c-abl oncogene 1, receptor tyrosine kinase | NM_007313 | 25 | 3.26 | Apoptosis, cell cycle, cell adhesion, actin cytoskeleton organization, peptidyl-tyrosine phosphorylation, transcription, signal transduction; intracellular |
| PRLH | Prolactin releasing hormone | NM_015893 | 51052 | 3.25 | Hormone activity; cytoplasm, extracellular |
| OASL | 2'-5'-oligoadenylate synthetase-like isoform a | NM_003733 | 8638 | 3.24 | ATP, DNA, double-stranded RNA binding, thyroid hormone receptor binding, transferase activity; cytoplasm, nucleus |
| HCP5 | HLA complex P5 | NM_006674 | 10866 | 3.23 | Defense response; plasma membrane |
| CCT6A | chaperonin containing TCP1, subunit 6A isoform a | NM_001762 | 908 | 3.22 | ATP, nucleotide, unfolded protein binding; cytoplasm |
| SMAD4 | SMAD family member 4 | NM_005359 | 4089 | 3.16 | R-SMAD, collagen binding, BMP signaling; cytosol, cytoplasm, nucleoplasm, nucleus |
| SMN2 | survival of motor neuron 2, centromeric | NM_022877 | 6607 | 3.15 | RNA, protein binding, RNA, mRNA splicing, cell death; cytosol, nucleus |
| CCL13 | chemokine (C-C motif) ligand 13 | NM_005408 | 6357 | 3.14 | chemokine activity, signal transducer activity, cell-cell signaling, inflammatory response; plasma membrane |
| TRIM23 | tripartite motif-containing 23 (ADP-ribosylation factor domain protein 1 isoform alpha) | NM_001656 | 373 | 3.14 | GDP, GTP, nucleotide binding; Golgi, cytoplasm |
| PFKFB2 | 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 2 isoform a | NM_006212 | 5208 | 3.13 | ATP, nucleotide binding, 6-phophofrukto-2-kinase hydrolase, kinase, transferase activity; cytosol |
| ERN1 | ER to nucleus signaling 1 isoform 2 | NM_152461 | 2081 | 3.08 | Endonuclease activity, cell cycle arrest, mRNA processing, regulation of transcription; ER, nuclear inner membrane |
| GABPB2 | GA binding protein transcription factor, beta subunit 2 isoform beta 1 | NM_005254 | 126626 | 3.07 | protein binding, transcription factor activity; nucleus |
| RAPGEF1 | Rap guanine nucleotide exchange factor (GEF) 1 (guanine nucleotide-releasing factor 2 isoform b | NM_198679 | 2889 | 3.06 | SH3 domain binding, guanyl-nucleotide exchange factor activity, protein binding; cytosol, endosome, intracellular |
| YTHDC1 | YTH domain containing protein 1 | NM_133370 | 91746 | 3.04 | RNA splicing, mRNA processing; nucleus |
| MORF4L1 | mortality factor 4 like 1 | NM_206839 | 10933 | 3.03 | DNA repair, chromatin modification, histone H2A acetylation, histone H4 acetylation, histone deacetylation; nucleus |
| SOX3 | SRY (sex determining region Y)-box 3 | NM_005634 | 6658 | 3.02 | DNA binding; nucleus |
| SNRPG | small nuclear ribonucleoprotein polypeptide G | NM_003096 | 6637 | 2.99 | RNA binding, RNA splicing, protein binding; cytosol, nucleus |
| POLR2K | DNA directed RNA polymerase II polypeptide | NM_005034 | 5440 | 2.98 | DNA binding, DNA-directed RNA polymerase activity, zinc ion binding; nucleoplasm, nucleus |
| ZMAT2 | zinc finger, matrin type 2 | NM_144723 | 153527 | 2.97 | DNA binding, zinc ion binding; intracellular, nucleus |
| AATK | apoptosis-associated tyrosine kinase | AK131529 | 9625 | 2.95 | ATP, nucleotide binding, transferase; cytoplasm, mitochondria |
| TSPAN13 | Tetraspanin 13 (TM4SF13, NET-6) | NM_014399 | 27075 | 2.90 | Plasma membrane |
| TAAR5 | trace amine associated receptor 5 (putative neurotransmitter receptor) | NM_003967 | 9038 | 2.88 | G-protein coupled receptor activity; plasma membrane |
| TMEM126A | transmembrane protein 126A | NM_032273 | 84233 | 2.87 | Molecular function; plasma membrane, mitochondria |
| COMP | cartilage oligomeric matrix protein precursor | NM_000095 | 1311 | 2.85 | calcium ion binding, ECM structure, cell adhesion; extracellular |
| ULBP2 | UL16 binding protein 2 | NM_025217 | 80328 | 2.80 | MHC class I receptor, NK cell activation; plasma membrane |
| ADAM7 | a disintegrin and metalloproteinase domain | NM_003817 | 8756 | 2.76 | metalloendopeptidase activity, zinc ion binding, proteolysis; plasma membrane |
| HUS1 | HUS1 checkpoint protein | NM_004507 | 3364 | 2.75 | protein binding, protein serine/threonine kinase activity, DNA repair, cell cycle; cytoplasm, nucleus |
| SH3KBP1 | SH3-domain kinase binding protein 1 (Homo sapiens migration-inducing gene 18 protein) | NM_031892 | 30011 | 2.74 | SH3 domain binding, protein binding, apoptosis, cell-cell signaling, endocytosis, focal adhesion; plasma membrane |
| PPM1B | protein phosphatase, Mg2+/Mn2+ dependent, 1B | NM_002706 | 5495 | 2.7 | hydrolase activity, magnesium ion binding, protein binding, protein serine/threonine phosphatase activity |
| SMURF1 | SMAD specific E3 ubiquitin protein ligase 1 | NM_020429 | 57154 | 2.68 | ubiquitin-protein ligase activity; cytoplasm, plasma membrane |
| SMPX | small muscle protein, X-linked | NM_014332 | 23676 | 2.63 | striated muscle contraction; cytoplasm, nucleus |
| ADAM21 | ADAM metallopeptidase domain 21 preproprotein | NM_003813 | 8747 | 2.63 | zinc ion binding, metalloendopeptidase activity, proteolysis, single fertilization; membrane |
| IGFALS | insulin-like growth factor binding protein, acid labile subunit | NM_004970 | 3483 | 2.62 | IGF binding, protein C-terminus binding, cell adhesion; extracellular region, microsome, soluble fraction |
| NPM1 | nucleophosmin (nucleolar phosphoprotein B23, numatrin) 1 isoform 2 | NM_199185 | 4869 | 2.62 | NF-kappaB, Tat protein, RNA, histone binding, protein hetero- or homodimerization, anti-apoptosis, cell-aging |
| ZNF407 | zinc finger protein 407 (KIAA1703 protein) | NM_017757 | 55628 | 2.61 | DNA, zinc ion binding, transcription; intracellular, nucleus |
| HLA-E | MHC, class I, E precursor | NM_005516 | 3133 | 2.61 | MHC class I receptor activity, antigen processing and presentation; plasma membrane |
| MOBKL3 | Mps One Binder kinase activator-like 3 (yeast) (preimplantation protein 3 isoform 1) | NM_015387 | 25843 | 2.59 | zinc ion, protein binding; Golgi, cytoplasma, membrane |
| B9D2 | B9 protein domain 2 (hypothetical LOC80776) | NM_030578 | 80776 | 2.57 | cell projection organization; cilium, microtubule basal body, nucleus |
| PEX6 | peroxisomal biogenesis factor 6 | NM_000287 | 5190 | 2.54 | ATPase activity, ATP, nucleotide, protein C-terminus binding; cytoplasm, cytosol, peroxisome |
| YWHAZ | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide | NM_145690 | 7534 | 2.52 | protein domain specific binding, transcription factor binding, anti- apoptosis; cytoplasm, mitochondria, nucleus |
| SUPV3L1 | suppressor of var1, 3-like 1 (S. cerevisiae) | NM_003171 | 6832 | 2.49 | ATP, DNA, RNA, nucleotide binding, DNA helicase activity, hydrolase activity, DNA duplex unwinding; nucleus, mitochondria |
| EIF2S1 | eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa | NM_004094 | 1965 | 2.48 | RNA, protein binding, translation initiation factor activity; cytoplasm, cytosol, nucleus |
| TUBA1B | tubulin, alpha 1b | NM_006082 | 10376 | 2.48 | GTP, protein binding, GTPase activity, microtubule cytoskeleton organization; microtubule |
| HNRPCL1 | heterogeneous nuclear ribonucleoprotein C-like 1 | NM_0010136 | 343069 | 2.48 | RNA binding, nucleotide binding; nucleus |
| POLB | polymerase (DNA directed), beta | NM_002690 | 5423 | 2.45 | DNA-directed DNA polymerase activity, damaged DNA binding, enzyme binding, lyase activity; cytoplasm, nucleoplasm, nucleus, spindle microtubule |
| SRPK3 | SFRS protein kinase 3 | NM_014370 | 26576 | 2.45 | ATP, nucleotide, protein binding, protein serine/threonine kinase activity, transferase activity; cellular component |
| TSPYL1 | TSPY-like 1 | NM_00309 | 7259 | 2.44 | Molecular function; intracellular, nucleolus, nucleus |
| RAI2 | retinoic acid induced 2 | NM_021785 | 10742 | 2.44 | Molecular function, embryonic development; cellular component |
| UQCR11 | ubiquinol-cytochrome c reductase, complex III subunit XI | NM_006830 | 10975 | 2.44 | electron carrier activity, ubiquinol-cytochrome-c reduction activity; mitochondria |
| POLDIP3 | polymerase (DNA-directed), delta interacting protein 3 | NM_032311 | 84271 | 2.41 | RNA binding, nucleotide binding, protein binding; nucleus |
| RPS14 | ribosomal protein S14 | NM_005617 | 6208 | 2.38 | RNA, mRNA 5'-UTR, protein binding, constituent of ribosome, translation regulator activity; cytosol, nucleolus, ribosome |
| SMCHD1 | structural maintenance of chromosomes flexible hinge domain containing 1 | NM_015295 | 23347 | 2.36 | ATP, protein binding; chromosome |
| HBS1L | HBS1(S. cerevisiae) -like translational GTPase | NM_006620 | 10767 | 2.32 | GTP, nucleotide binding, GTPase activity, translation elongation factor activity |
| SLC4A3 | solute carrier family 4, anion exchanger, member 3 | NM_001326559 | 6508 | 2.22 | anion transmembrane transporter activity; inorganic anion exchanger activity; transporter activity; plasma membrane |
| DEGs down-regulated only in HAM/TSP | |||||
| Gene Symbol | Product | Accession number | Gene ID |
Relative expression (fold change) |
Function and localization |
| N/A | ih08h09.x1 Human insulinoma Homo sapiens cDNA 3', mRNA sequence | BM310182.1 | N/A | 0.30 | Unknown. Transcribed locus from EST. |
| N/A | Homo sapiens cDNA FLJ37957 fis, clone CTONG2009 529 | AK095276.1 | N/A | 0.32 | Unknown. hypothetical protein LOC283588. |
| MAP7D3 | MAP7 domain containing 3 [Homo sapiens] | AL832120 | 79649 | 0.36 | Member of MAP7 (microtubule-associated protein 7) family. microtubule polymerization and stabilization; cancer growth and metastasis. |
| ARFGEF2 | ADP-ribosylation factor guanine nucleotide-exchange factor 2 [Homo sapiens] | NM_006420 | 10564 | 0.49 | Intracellular vesicular trafficking. activation of ARFs by accelerating replacement of bound GDP with GTP and is involved in Golgi transport; guanine-nucleotide exchange activity and also brefeldin A inhibition. |
The accession numbers are numbers of the longest variant as representative when there are multiple variants. N/A: not applicable.