Table 1.
Gene symbol | Name | RefSeq ID | Log2(TDP-43 cKO/ Ctrl) | Significant (q<0.05) | FTLD patient | White et al. [86] | Other references | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
3 Months | 12 months | 3 Months | 12 months | 5 Months frontal cortex | 20 Months frontal cortex | |||||||
Common | MB- | Common | MB- | |||||||||
Rabggtb | Rab geranylgeranyltransferase beta subunit | NM_011231 | 6.21 | -0.14 | ● | |||||||
Clec7a | C-type lectin domain containing 7A | NM_020008 | 4.06 | 2.09 | ● | (Chen-Plotkin et al. [17]) | ||||||
Itgad | Integrin alpha-D | NM_001029872 | 2.99 | 1.45 | ● | |||||||
Brd3 | bromodomain containing 3 | NM_023336 | 2.88 | 0.11 | ● | |||||||
Atf3 | activating transcription factor 3 | NM_007498 | 2.47 | 1.90 | ● | |||||||
Slc6a3 | solute carrier family 6 member 3 | NM_010020 | 2.19 | 0.80 | ● | |||||||
Ccl9 | chemokine (C-C motif) ligand 6 | NM_011338 | 2.15 | 0.15 | ● | |||||||
Ccl6 | chemokine (C-C motif) ligand 9 | NM_009139 | 2.09 | 0.18 | ● | |||||||
Cep112 | centrosomal protein 112 | NM_029586 | 1.76 | 0.04 | ● | |||||||
Pafah2 | platelet-activating factor acetylhydrolase 2 | NM_001285872 | 1.69 | 1.50 | ● | |||||||
Tlr2 | toll like receptor 2 | NP_036035 | 1.66 | 0.88 | ● | |||||||
Oasl2 | 2'-5' oligoadenylate synthetase-like 2 | NM_011854 | 1.61 | 0.85 | ● | |||||||
Lag3 | lymphocyte-activation gene 3 | NM_008479 | 1.55 | 0.17 | ● | ● | ||||||
C3ar1 | complement C3a receptor 1 | NP_033909 | 1.52 | 0.18 | ● | (Chen-Plotkin et al. [17]) | ||||||
Lyz1,Lyz2 | lysozyme 1 | NM_017372 | 1.48 | 0.86 | ● | |||||||
Ddhd1 | DDHD domain containing 1 | NM_176845 | 1.44 | 0.13 | ● | |||||||
Myo1f | myosin IF | NM_053214 | 1.39 | 0.60 | ● | ● | ||||||
Trem2 | triggering receptor expressed on myeloid cells 2 | NM_001272078 | 1.16 | 0.25 | ● | (Polymenidou et al. [58]) | ||||||
Ptpn6 | protein tyrosine phosphatase, non-receptor type 6 | NM_001077705 | 1.15 | 0.63 | ● | ● | ||||||
Ifit3b | interferon-induced protein with tetratricopeptide repeats 3B | NM_001005858 | 1.11 | 0.31 | ● | (Polymenidou et al. [58]) | ||||||
C1qa | complement component 1, q subcomponent, alpha polypeptide | NM_007572 | 1.02 | 0.42 | ● | (Polymenidou et al. [58]) | ||||||
Tyrobp | TYRO protein tyrosine kinase binding protein | NM_011662 | 1.01 | 0.19 | ● | (Polymenidou et al. [58]) | ||||||
Lgals3bp | lectin, galactoside-binding, soluble, 3 binding protein | NM_011150 | 0.99 | 0.38 | ● | (Chen-Plotkin et al. [17]) | ||||||
C1qb | complement component 1, q subcomponent, beta polypeptide | NM_009777 | 0.96 | 0.41 | ● | ● | (Polymenidou et al. [58]) | |||||
C1qc | complement component 1, q subcomponent, C chain | NM_007574 | 0.90 | 0.39 | ● | ● | ||||||
Fcrls | Fc receptor-like S, scavenger receptor | NM_030707 | 0.91 | -0.11 | ● | ● | ||||||
Fcgr3 | Fc receptor, IgG, low affinity III | NM_010188 | 0.83 | 0.53 | ● | ● | (Polymenidou et al. [58]) | |||||
Ctss | cathepsin S | NM_001267695 | 0.79 | 0.28 | ● | (Polymenidou et al. [58]) | ||||||
Ripor1 | Rho family interacting cell polarization regulator 1 | NM_001081241 | -1.48 | -0.28 | ● | |||||||
Plod3 | procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 | NM_011962 | -1.23 | 0.14 | ● | ● | ||||||
Hist1h4m | histone cluster 1, H4m | NM_175654 | -1.18 | -0.30 | ● | |||||||
Zfp101 | zinc finger protein 101 | NM_009542 | -1.02 | -0.26 | ● | ● | ||||||
Dlg3 | discs large MAGUK scaffold protein 3 | NM_007863 | -0.87 | 0.00 | ● | (Chen-Plotkin et al. [17]) | (LaClair et al. [43]) | |||||
Otof | otoferlin | NM_001100395 | -0.86 | -0.34 | ● | ● (up) | ||||||
Dock4 | dedicator of cytokinesis 4 | NM_172803 | -0.79 | -0.52 | ● | ● | (Polymenidou et al. [58]) | |||||
Abr | active BCR-related gene | NM_001291186 | -0.79 | -0.41 | ● | (LaClair et al. [43]) | ||||||
Syt17 | synaptotagmin XVII | NM_138649 | -0.70 | -0.48 | ● | |||||||
Unc13a | unc-13 homolog A (C. elegans) | NP_001025044 | -0.77 | -0.48 | ● | (Polymenidou et al. [58]) | ||||||
Rab11fip5 | RAB11 family interacting protein 5 (class I) | NM_001003955 | -0.69 | -0.58 | ● | |||||||
Fgf21 | fibroblast growth factor 21 | NM_020013 | 0.00 | 0.00 | ● | |||||||
Gfap | glial fibrillary acidic protein | NM_001131020 | 1.74 | 1.43 | ● | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | ||||
Serpina3n | serine (or cysteine) peptidase inhibitor, clade A, member 3N | NP_035588 | 1.27 | 1.34 | ● | ● | ||||||
C4a,C4b | complement component 4a/b | NM_011413 | 1.64 | 1.46 | ● | ● | (Chen-Plotkin et al. [17]) | |||||
A2m | alpha-2-macroglobulin | NM_175628 | 1.37 | 2.09 | ● | ● | ||||||
Tecpr1 | tectonin beta-propeller repeat containing 1 | NP_081686 | -1.06 | -0.93 | ● | ● | (LaClair et al. [43]) | |||||
Tarsl2 | threonyl-tRNA synthetase-like 2 | NM_172310 | -1.00 | -0.90 | ● | ● | ||||||
Pitpnm3 | PITPNM family member 3 | NM_001024927 | -0.97 | -0.96 | ● | ● | ● (up) | ● (up) | (LaClair et al. [43]) | |||
Epop | elongin BC and polycomb repressive complex 2 associated protein | NM_175332 | -0.80 | -0.90 | ● | ● | ||||||
Arc | activity regulated cytoskeletal-associated protein | NM_001276684 | -0.84 | -0.80 | ● | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | ||||
Cry2 | cryptochrome 2 (photolyase-like) | NM_009963 | -0.78 | -0.58 | ● | ● | ||||||
Lamp5 | lysosomal-associated membrane protein family, member 5 | NM_029530 | -0.71 | -0.96 | ● | ● | ||||||
Fam171a2 | family with sequence similarity 171, member A2 | NM_199200 | -0.70 | -0.65 | ● | ● | ● | |||||
Oxt | oxytocin/neurophysin I prepropeptide | NM_011025 | 1.11 | 2.95 | ● | |||||||
Plin4 | perilipin 4 | NM_020568 | 0.61 | 1.85 | ● | ● | ||||||
Irs4 | insulin receptor substrate 4 | NP_034702 | 0.22 | 1.79 | ● | |||||||
Itih3 | inter-alpha trypsin inhibitor, heavy chain 3 | NM_008407 | 0.69 | 1.27 | ● | |||||||
Etnppl | ethanolamine phosphate phospholyase | NM_001163587 | 0.63 | 1.07 | ● | |||||||
AW551984 | expressed sequence AW551984 | NM_001199556 | 0.08 | 1.04 | ● | |||||||
Agt | angiotensinogen (serpin peptidase inhibitor, clade A, member 8) | NM_007428 | 0.31 | 0.97 | ● | ● | ||||||
Chd1l | chromodomain helicase DNA binding protein 1-like | NM_026539 | -0.16 | 0.96 | ● | |||||||
Uggt2 | UDP-glucose glycoprotein glucosyltransferase 2 | NM_001081252 | 0.26 | 0.87 | ● | ● | ||||||
Vip | vasoactive intestinal polypeptide | NM_001313969 | 0.57 | 0.79 | ● | |||||||
Sparc | secreted acidic cysteine rich glycoprotein | NM_001290817 | 0.48 | 0.77 | ● | (Chen-Plotkin et al. [17]) | ● | ● (down) | ||||
Baiap3 | BAI1-associated protein 3 | NM_001163270 | 0.24 | 0.72 | ● | |||||||
Nnat | neuronatin | NM_001291128 | 0.37 | 0.70 | ● | |||||||
Fam107a | family with sequence similarity 107, member A | NM_183187 | 0.38 | 0.69 | ● | |||||||
Sdc4 | syndecan 4 | NM_011521 | 0.33 | 0.68 | ● | ● | (Polymenidou et al. [58]) | |||||
Ptgds | prostaglandin D2 synthase (brain) | NM_008963 | 0.27 | 0.65 | ● | (Chen-Plotkin et al. [17]) | ||||||
Scg2 | secretogranin II | NM_001310680 | 0.21 | 0.58 | ● | (Chen-Plotkin et al. [17]) | ||||||
Apod | apolipoprotein D | NM_001301353 | 0.38 | 0.54 | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | |||||
Tnnc1 | troponin C1, slow skeletal and cardiac type | NP_033419 | -1.20 | -2.38 | ● | |||||||
Gm10635 | predicted gene 10635 | NR_045336 | -1.10 | -2.42 | ● | |||||||
Mylk3 | myosin light chain kinase 3 | NM_175441 | -1.04 | -2.28 | ● | ● | ||||||
Mecom | MDS1 and EVI1 complex locus | NM_007963 | 0.05 | -1.76 | ● | |||||||
Rspo1 | R-spondin 1 | NP_619624 | -0.80 | -1.46 | ● | |||||||
Myl4 | myosin, light polypeptide 4 | NM_010858 | -0.29 | -1.36 | ● | (Polymenidou et al. [58]) | ||||||
Ddit4l | DNA-damage-inducible transcript 4-like | NM_030143 | -0.65 | -1.13 | ● | |||||||
Grm2 | glutamate receptor, metabotropic 2 | NM_001160353 | -0.52 | -1.12 | ● | |||||||
Cpne9 | copine family member IX | NM_170673 | -0.70 | -1.04 | ● | |||||||
Ryr1 | ryanodine receptor 1 | NP_033135 | -0.58 | -0.98 | ● | ● (up) | ||||||
Rassf3 | Ras association domain family member 3 | NP_620406 | -0.26 | -0.91 | ● | |||||||
Egr1 | early growth response 1 | NM_007913 | -0.42 | -0.90 | ● | (Chen-Plotkin et al. [17]) | ● (down) | |||||
Kcnt2 | potassium channel, subfamily T, member 2 | NM_001081027 | -0.54 | -0.89 | ● | ● | ||||||
Rims3 | regulating synaptic membrane exocytosis 3 | NM_182929 | -0.38 | -0.84 | ● | ● | (Polymenidou et al. [58]) | |||||
Pisd-ps3 | phosphatidylserine decarboxylase, pseudogene 3 | NR_003518 | 0.10 | -0.86 | ● | |||||||
Kcnab3 | potassium voltage-gated channel, shaker-related subfamily, beta member 3 | NM_010599 | -0.11 | -0.86 | ● | (Polymenidou et al. [58]) | ||||||
Fos | FBJ osteosarcoma oncogene | NM_010234 | -0.77 | -0.84 | ● | |||||||
Scube1 | signal peptide, CUB domain, EGF-like 1 | NM_001271472 | -0.43 | -0.83 | ● | ● (up) | ||||||
Kcnh5 | potassium voltage-gated channel, subfamily H (eag-related), member 5 | NM_172805 | -0.45 | -0.83 | ● | |||||||
Inf2 | inverted formin, FH2 and WH2 domain containing | NM_198411 | -0.35 | -0.83 | ● | |||||||
Acvr1c | activin A receptor, type IC | NM_001111030 | -0.13 | -0.82 | ● | |||||||
Hipk4 | homeodomain interacting protein kinase 4 | NP_001028487 | -0.51 | -0.81 | ● | |||||||
Scrt1 | scratch family zinc finger 1 | NM_130893 | -0.26 | -0.77 | ● | |||||||
Hapln4 | hyaluronan and proteoglycan link protein 4 | NM_177900 | -0.47 | -0.75 | ● | (Polymenidou et al. [58]) | ||||||
Kif5a | kinesin family member 5A | NM_001039000 | -0.52 | -0.76 | ● | |||||||
Arhgap10 | Rho GTPase activating protein 10 | NP_001074833 | 0.00 | -0.75 | ● | |||||||
Camk2n1 | calcium/calmodulin-dependent protein kinase II inhibitor 1 | NM_025451 | -0.40 | -0.74 | ● | ● | ● (down) | |||||
Car10 | carbonic anhydrase 10 | NP_082572 | -0.33 | -0.73 | ● | |||||||
Camk4 | calcium/calmodulin-dependent protein kinase IV | NM_009793 | -0.24 | -0.73 | ● | ● | (Polymenidou et al. [58]) | |||||
Rims1 | regulating synaptic membrane exocytosis 1 | NM_001012623 | -0.42 | -0.73 | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | |||||
Eipr1 | EARP complex and GARP complex interacting protein 1 | NM_201357 | -0.68 | -0.73 | ● | (Polymenidou et al. [58]) | ||||||
Rgs4 | regulator of G-protein signaling 4 | NM_009062 | -0.52 | -0.73 | ● | (Chen-Plotkin et al. [17]) | ||||||
Rapgef4 | Rap guanine nucleotide exchange factor (GEF) 4 | NM_001204165 | -0.23 | -0.70 | ● | ● (down) | ||||||
Dagla | diacylglycerol lipase, alpha | NM_198114 | -0.43 | -0.69 | ● | |||||||
Diras2 | DIRAS family, GTP-binding RAS-like 2 | NM_001024474 | -0.52 | -0.69 | ● | (Chen-Plotkin et al. [17]) | ||||||
Gp1bb | glycoprotein Ib, beta polypeptide | NM_001001999 | -0.65 | -0.68 | ● | |||||||
Ano3 | anoctamin 3 | NM_001128103 | -0.33 | -0.67 | ● | ● | ||||||
Grm3 | glutamate receptor, metabotropic 3 | NM_181850 | -0.26 | -0.67 | ● | |||||||
Nefm | neurofilament, medium polypeptide | NM_008691 | -0.53 | -0.66 | ● | (Polymenidou et al. [58]) | ||||||
Gabra3 | gamma-aminobutyric acid (GABA) A receptor, subunit alpha 3 | NM_008067 | -0.57 | -0.65 | ● | (Polymenidou et al. [58]) | ||||||
Rph3a | rabphilin 3A | NM_001302344 | -0.39 | -0.65 | ● | (Chen-Plotkin et al. [17]) | ||||||
Tbr1 | T-box brain gene 1 | NM_009322 | -0.51 | -0.63 | ● | (Polymenidou et al. [58]) | ||||||
Satb1 | special AT-rich sequence binding protein 1 | NM_001163630 | -0.39 | -0.64 | ● | |||||||
Sh3gl2 | SH3-domain GRB2-like 2 | NM_019535 | -0.22 | -0.63 | ● | (Chen-Plotkin et al. [17]) | ||||||
Ephb6 | Eph receptor B6 | NM_001146351 | -0.37 | -0.63 | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | |||||
Kcnh3 | potassium voltage-gated channel, subfamily H (eag-related), member 3 | NM_010601 | -0.43 | -0.62 | ● | |||||||
Nrgn | neurogranin | NM_022029 | -0.35 | -0.62 | ● | (Chen-Plotkin et al. [17]) | ||||||
Cadm2 | cell adhesion molecule 2 | NM_001145977 | -0.17 | -0.61 | ● | ● | ||||||
Camkk2 | calcium/calmodulin-dependent protein kinase kinase 2, beta | NM_001199676 | -0.44 | -0.61 | ● | (Chen-Plotkin et al. [17]) | ||||||
Rorb | RAR-related orphan receptor beta | NM_001043354 | -0.34 | -0.60 | ● | |||||||
Scn4b | sodium channel, type IV, beta | NP_001013408 | 0.05 | -0.60 | ● | ● | ||||||
Camk2a | calcium/calmodulin-dependent protein kinase II alpha | NM_001286809 | -0.50 | -0.60 | ● | (Chen-Plotkin et al. [17]) | ||||||
Nrn1 | neuritin 1 | NM_153529 | -0.24 | -0.60 | ● | (Chen-Plotkin et al. [17]) | ||||||
Cdk5r2 | cyclin-dependent kinase 5, regulatory subunit 2 (p39) | NM_009872 | -0.42 | -0.60 | ● | |||||||
Rbfox3 | RNA binding protein, fox-1 homolog (C. elegans) 3 | NM_001024931 | -0.34 | -0.60 | ● | |||||||
Gca | grancalcin | NP_663498 | 0.08 | -0.59 | ● | |||||||
Osbpl1a | oxysterol binding protein-like 1A | NM_001252489 | -0.39 | -0.59 | ● | ● | ||||||
Vsnl1 | visinin-like 1 | NM_012038 | -0.32 | -0.59 | ● | (Chen-Plotkin et al. [17]) | ● | |||||
Adcy1 | adenylate cyclase 1 | NM_009622 | -0.25 | -0.59 | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | |||||
Neurod6 | neurogenic differentiation 6 | NM_009717 | -0.41 | -0.59 | ● | (Polymenidou et al. [58]) | ||||||
AI593442 | expressed sequence AI593442 | NM_001286641 | -0.19 | -0.58 | ● | |||||||
Stx1a | syntaxin 1A (brain) | NM_016801 | -0.28 | -0.57 | ● | (Chen-Plotkin et al. [17]) | (Polymenidou et al. [58]) | |||||
Nat8l | N-acetyltransferase 8-like | NP_001001985 | -0.34 | -0.57 | ● | |||||||
3110035E14Rik | RIKEN cDNA 3110035E14 gene | NM_178399 | -0.28 | -0.57 | ● | (Polymenidou et al. [58]) | ||||||
Zbtb18 | zinc finger and BTB domain containing 18 | NM_001012330 | -0.22 | -0.57 | ● | |||||||
Hlf | hepatic leukemia factor | NM_172563 | -0.39 | -0.56 | ● | |||||||
Lynx1 | Ly6/neurotoxin 1 | NM_011838 | -0.28 | -0.56 | ● | (Polymenidou et al. [58]) | ||||||
Cadps2 | Ca2+-dependent activator protein for secretion 2 | NM_001252105 | -0.53 | -0.56 | ● | |||||||
Psd | pleckstrin and Sec7 domain containing | NM_133694 | -0.47 | -0.56 | ● | |||||||
Dhcr24 | 24-dehydrocholesterol reductase | NM_053272 | -0.49 | -0.54 | ● | ● | ||||||
2900011O08Rik | RIKEN cDNA 2900011O08 gene | NM_144518 | -0.53 | -0.53 | ● | |||||||
Dlgap3 | discs, large (Drosophila) homolog-associated protein 3 | NM_001302081 | -0.43 | -0.52 | ● | (Polymenidou et al. [58]) | ||||||
Bhlhe40 | basic helix-loop-helix family, member e40 | NM_011498 | -0.35 | -0.53 | ● | |||||||
Pcp4 | Purkinje cell protein 4 | NM_008791 | -0.04 | -0.52 | ● | (Chen-Plotkin et al. [17]) | ● | |||||
Cntnap1 | contactin associated protein-like 1 | NM_016782 | -0.38 | -0.52 | ● | (Chen-Plotkin et al. [17]) | ||||||
Cep170b | centrosomal protein 170B | NM_001024602 | -0.42 | -0.51 | ● | |||||||
Plcxd2 | phosphatidylinositol-specific phospholipase C, X domain containing 2 | NM_001134480 | -0.16 | -0.50 | ● | |||||||
Cplx2 | complexin 2 | NM_009946 | -0.26 | -0.50 | ● | |||||||
Phyhip | phytanoyl-CoA hydroxylase interacting protein | NM_145981 | -0.38 | -0.50 | ● | (Chen-Plotkin et al. [17]) | ||||||
Snap25 | synaptosomal-associated protein 25 | NM_001291056 | -0.43 | -0.50 | ● | (Chen-Plotkin et al. [17]) | ||||||
Slc8a2 | solute carrier family 8 (sodium/calcium exchanger), member 2 | NM_001347561 | -0.42 | -0.50 | ● | (Chen-Plotkin et al. [17]) | ||||||
D430041D05Rik | RIKEN cDNA D430041D05 gene | NM_001033347 | -0.47 | -0.49 | ● | |||||||
Tubb4a | tubulin, beta 4A class IVA | NM_009451 | -0.38 | -0.49 | ● | |||||||
Ppp3r1 | protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) | NM_024459 | -0.25 | -0.48 | ● | (Chen-Plotkin et al. [17]) | ● | |||||
Epdr1 | ependymin related protein 1 (zebrafish) | NM_134065 | -0.35 | -0.48 | ● | ● | ● | |||||
Scn1b | sodium channel, voltage-gated, type I, beta | NM_011322 | -0.20 | -0.47 | ● | |||||||
Jph3 | junctophilin 3 | NM_020605 | -0.39 | -0.47 | ● | ● | ||||||
Syt13 | synaptotagmin XIII | NM_030725 | -0.33 | -0.45 | ● | ● | (Polymenidou et al. [58]) | |||||
Snap91 | synaptosomal-associated protein 91 | NM_001277982 | -0.53 | -0.45 | ● | (Chen-Plotkin et al. [17]) | ||||||
Zfp365 | zinc finger protein 365 | NM_178679 | -0.24 | -0.44 | ● | |||||||
Atp1a1 | ATPase, Na+/K+ transporting, alpha 1 polypeptide | NM_144900 | -0.33 | -0.44 | ● |
The down-regulated genes are indicated by the "-" sign in the columns of Log2 (TDP-43 cKO/Ctrl). The genes that have been reported to have altered mRNA levels in the FTLD patients and in the striatum or hippocampus upon TDP-43 depletion are indicated in the far right column