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Table 4 List of significant genes with a significant protein

From: RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

Gene/protein

UniProt accession

Gene fold change

Protein fold change

RTT hit?

Putative function

Mecp2/MeCP2

Q9Z2D6

− 0.66

− 10.6

Yes1, 2

DNA binding protein; transcriptional regulator

Rnpep/RNPEP*

Q8VCT3

− 0.78

− 3.47

Yes2

Peptide catabolic process

Pdia4/ERp72*

P08003

− 0.71

− 2.22

Yes2,3

ER protein processing

Hsph1/HSPH1

Q61699

− 0.80

− 2.13

Yes4

Protein chaperone

Rnpep/RNPEP(Ac)*

Q8VCT3

− 0.78

− 2.02

Yes2

Peptide catabolic process

Aldh1a1/ALDH1A1*

P24549

− 0.67

− 1.95

Yes2

Retinal dehydrogenase

Slc9a3r1/NHERF1(P)*

P70441

− 0.74

− 1.79

Yes3

Scaffold protein

Ugt8a/UGT8

Q64676

− 0.79

− 1.76

---

Sphingolipid metabolism

Qdpr/QDPR (or DHPR)*

Q8BVI4

− 0.74

− 1.68

Yes2

Monoamine metabolism (tetrahydrobiopterin biosynthesis)

Ugp2/UGP2*

Q91ZJ5

− 0.73

− 1.67

Yes2

Glycogen synthesis

Car2/Ca2

P00920

− 0.72

− 1.61

---

Reversible hydration of carbon dioxide

Grm3/mGluR3*

Q9QYS2

− 0.63

− 1.6

Yes2

Protein coupled glutamate receptor

Ephx2/EPHX2*

P34914

− 0.71

− 1.59

Yes2

Cholesterol synthesis

Hpcal4/HPCAL4*

Q8BGZ1

− 0.69

− 1.51

Yes2,3

Calcium binding

Spr/SPR

Q64105

− 0.77

− 1.47

---

Monoamine metabolism (tetrahydrobiopterin metabolic process)

Sash1/SASH1

P59808

− 0.82

− 1.44

---

p38 MAPK and NIK/NF-kappaB signaling

Calr/CRT*

P14211

− 0.80

− 1.43

Yes3

ER calcium-binding protein

Aacs/AACS*

Q9D2R0

− 0.79

− 1.37

Yes2

Fatty acid and lipid metabolism

S1pr1/S1P1

O08530

− 0.78

− 1.28

---

Cell-cell adhesion

Slc9a3r1/NHERF1(Ac)*

P70441

− 0.74

− 1.24

Yes3

Scaffold protein

Nova1/NOVA1

Q9JKN6

1.26

1.28

---

RNA/mRNA-binding protein

Slc24a4/Nckx4*

Q8CGQ8

1.58

1.3

Yes3

K+-dependent Na+/Ca2+ exchanger

Kcnab3/Kvβ3.1

P97382

1.27

1.43

---

Voltage gated K+ channel

Me3/NADP-ME3

Q8BMF3

1.28

1.46

---

Mitochondrial NADP(+)-dependent malic enzyme

Tfrc/TfR

Q62351

1.32

1.48

---

Cell surface receptor required for iron uptake

Dgkg/DGKγ*

Q91WG7

1.42

1.51

Yes2,3

Lipid metabolism

Prkcg/PKCγ(P)*

P63318

− 0.82

1.66

Yes3

Protein kinase; LTP

Rasgrf1/RasGRF1

P27671

1.32

1.68

---

Stimulates the dissociation of GDP from RAS protein

Zmat4/ZMAT4*

Q8BZ94

1.50

1.88

Yes3

DNA/RNA and p53 binding

Myo1b/Myo1b*

P46735

1.32

2.02

Yes2,3

Actin binding; calmodulin binding

Fkbp5/FKBP5

Q64378

1.81

2.02

Yes2–6

Immunoregulation; protein trafficking

Wipf3/WIPF3

P0C7L0

1.23

2.26

---

Cytoskeleton organization

Itih3/ITI-HC3

Q61704

1.52

2.37

---

Anchor protein between hyaluronan and matrix proteins

Gfra1/GDNFRα1*

P97785

1.26

2.64

Yes2,3

RET and RAF/MAP kinase signaling cascade

Sun2/SUN2*

Q8BJS4

1.42

2.86

Yes3

Nuclear envelope protein

  1. Significant genes were defined as having a q < 0.05, and significant proteins having a p < 0.1. Gene and protein names are provided along with the UniProt accession number, gene and protein fold change expression values (respectively), whether the gene-protein match has been previously identified as a RTT hit, and the respective putative function according to the UniProtKB/Swiss-Prot database [131]. DE gene-protein matches with an asterisk (*) represent genes/proteins identified in supplemental material from Chahrour et al. [4] and Veeraragavan et al. [34]. Gene-protein matches with “(Ac)” denote that the corresponding protein had a significant acetylation PTM, and a “(P)” denotes a significant phosphorylation PTM. For the RTT hit column, a “---” indicates the match has not been identified as a RTT hit prior to this study. Superscripts in the RTT hit column denote references for matches identified as a RTT hit and are as follows: (1) Amir et al. [2], (2) Chahrour et al. [4], (3) Veeraragavan et al. [34], (4) Nuber et al. [21], (5) Urdinguio et al. [24], and (6) Lin et al. [33]