Table 1 The genes with altered mRNA levels in the neocortex of 3-month and 12-month-old TDP-43 cKO mice in comparison to the Ctrls are listed

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

●