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Table 3 68 upregulated and 18 downregulated genes in JHC7-CMTM3 cells vs. JHC7-MOCK cells (padj < 0.001)

From: CMTM3 suppresses chordoma progress through EGFR/STAT3 regulated EMT and TP53 signaling pathway

Gene ID

Gene name

Gene description

Log2 fold change (CMTM3/MOCK)

padj

Upregulated DEGs

 ENSG00000140931

CMTM3

CKLF like MARVEL transmembrane domain containing 3

12.25

6.90E−105

 ENSG00000141510

TP53

Tumor protein p53

11.14

9.02E−105

 ENSG00000173110

HSPA6

Heat shock protein family A (Hsp70) member 6

9.65

4.80E−88

 ENSG00000106211

HSPB1

Heat shock protein family B (small) member 1

5.42

2.11E−55

 ENSG00000204388

HSPA1B

Heat shock protein family A (Hsp70) member 1B

6.41

1.53E−40

 ENSG00000204389

HSPA1A

Heat shock protein family A (Hsp70) member 1A

6.93

5.06E−39

 ENSG00000132002

DNAJB1

DnaJ heat shock protein family (Hsp40) member B1

4.66

6.02E−25

 ENSG00000149257

SERPINH1

Serpin family H member 1

3.61

7.00E−24

 ENSG00000105550

FGF21

Fibroblast growth factor 21

4.44

2.35E−19

 ENSG00000151929

BAG3

BCL2 associated athanogene 3

3.53

6.39E−19

 ENSG00000120694

HSPH1

Heat shock protein family H (Hsp110) member 1

3.50

9.56E−16

 ENSG00000109846

CRYAB

Crystallin alpha B

3.51

8.51E−14

 ENSG00000130513

GDF15

Growth differentiation factor 15

2.66

5.81E−13

 ENSG00000080824

HSP90AA1

Heat shock protein 90 alpha family class A member 1

3.77

1.56E−12

 ENSG00000100292

HMOX1

Heme oxygenase 1

4.62

7.00E−12

 ENSG00000004478

FKBP4

FK506 binding protein 4

2.56

9.83E−11

 ENSG00000109971

HSPA8

Heat shock protein family A (Hsp70) member 8

2.70

7.19E−09

 ENSG00000130766

SESN2

Sestrin 2 [Source:HGNC Symbol;Acc:HGNC:20746]

2.24

8.27E−09

 ENSG00000099875

MKNK2

MAP kinase interacting serine/threonine kinase 2

2.39

3.77E−07

 ENSG00000100591

AHSA1

Activator of HSP90 ATPase activity 1

2.07

5.39E−07

 ENSG00000188483

IER5L

Immediate early response 5 like

2.72

6.14E−07

 ENSG00000168439

STIP1

Stress induced phosphoprotein 1

2.35

3.19E−06

 ENSG00000168209

DDIT4

DNA damage inducible transcript 4

2.71

3.41E−06

 ENSG00000174951

FUT1

Fucosyltransferase 1 (H blood group)

2.45

3.48E−06

 ENSG00000115541

HSPE1

Heat shock protein family E (Hsp10) member 1

2.14

3.58E−06

 ENSG00000128965

CHAC1

ChaC glutathione specific gamma-glutamylcyclotransferase 1

2.56

3.90E−06

 ENSG00000116161

CACYBP

Calcyclin binding protein

2.16

4.86E−06

 ENSG00000224411

HSP90AA2P

Heat shock protein 90 alpha family class A member 2, pseudogene

3.45

6.23E−06

 ENSG00000178381

ZFAND2A

Zinc finger AN1-type containing 2A

1.98

8.53E−06

 ENSG00000110680

CALCA

Calcitonin related polypeptide alpha

8.18

8.98E−06

 ENSG00000087074

PPP1R15A

Protein phosphatase 1 regulatory subunit 15A

2.47

9.76E−06

 ENSG00000175084

DES

Desmin

2.42

9.94E−06

 ENSG00000086061

DNAJA1

DnaJ heat shock protein family (Hsp40) member A1

2.01

9.94E−06

 ENSG00000121068

TBX2

T-box 2

2.47

1.06E−05

 ENSG00000162783

IER5

Immediate early response 5

1.91

1.06E−05

 ENSG00000121769

FABP3

Fatty acid binding protein 3

2.16

1.06E−05

 ENSG00000096384

HSP90AB1

Heat shock protein 90 alpha family class B member 1

2.18

1.43E−05

 ENSG00000161180

CCDC116

Coiled-coil domain containing 116

4.54

1.75E−05

 ENSG00000258469

CHMP4BP1

Charged multivesicular body protein 4B pseudogene 1

3.80

2.01E−05

 ENSG00000028277

POU2F2

POU class 2 homeobox 2

3.27

2.38E−05

 ENSG00000110172

CHORDC1

Cysteine and histidine rich domain containing 1

2.21

3.93E−05

 ENSG00000008517

IL32

Interleukin 32

2.40

4.39E−05

 ENSG00000139269

INHBE

Inhibin subunit beta E

3.70

4.39E−05

 ENSG00000087086

FTL

Ferritin light chain

2.01

4.95E−05

 ENSG00000144381

HSPD1

Heat shock protein family D (Hsp60) member 1

1.98

5.26E−05

 ENSG00000225217

HSPA7

Heat shock protein family A (Hsp70) member 7

7.46

5.27E−05

 ENSG00000101255

TRIB3

Tribbles pseudokinase 3

2.20

5.27E−05

 ENSG00000116717

GADD45A

Growth arrest and DNA damage inducible alpha

1.79

5.27E−05

 ENSG00000149781

FERMT3

Fermitin family member 3

3.99

5.98E−05

 ENSG00000183696

UPP1

Uridine phosphorylase 1

1.80

6.76E−05

 ENSG00000064300

NGFR

Nerve growth factor receptor

3.84

1.04E−04

 ENSG00000164045

CDC25A

Cell division cycle 25A

1.93

1.05E−04

 ENSG00000200879

SNORD14E

Small nucleolar RNA, C/D box 14E

5.05

1.10E−04

 ENSG00000148926

ADM

Adrenomedullin

2.24

1.20E−04

 ENSG00000167513

CDT1

Chromatin licensing and DNA replication factor 1

2.02

1.20E−04

 ENSG00000282855

AC093591.3

INTS3 and NABP interacting protein (INIP) pseudogene

4.03

1.43E−04

 ENSG00000123358

NR4A1

Nuclear receptor subfamily 4 group A member 1

2.01

1.74E−04

 ENSG00000211891

IGHE

Immunoglobulin heavy constant epsilon

6.74

1.96E−04

 ENSG00000131094

C1QL1

Complement C1q like 1

1.69

2.43E−04

 ENSG00000105219

CNTD2

Cyclin N-terminal domain containing 2

2.56

3.06E−04

 ENSG00000088826

SMOX

Spermine oxidase

1.76

4.19E−04

 ENSG00000068028

RASSF1

Ras association domain family member 1

1.89

4.19E−04

 ENSG00000175183

CSRP2

Cysteine and glycine rich protein 2

2.22

5.01E−04

 ENSG00000213430

HSPD1P1

Heat shock protein family D (Hsp60) member 1 pseudogene 1

2.20

5.33E−04

 ENSG00000237596

AL138828.1

Novel transcript

3.98

6.21E−04

 ENSG00000127564

PKMYT1

Protein kinase, membrane associated tyrosine/threonine 1

2.14

7.75E−04

 ENSG00000066735

KIF26A

Kinesin family member 26A

2.13

9.19E−04

 ENSG00000164070

HSPA4L

Heat shock protein family A (Hsp70) member 4 like

1.99

9.97E−04

Downregulated DEGs

 ENSG00000147724

FAM135B

Family with sequence similarity 135 member B

− 2.91

1.04E−07

 ENSG00000147041

SYTL5

synaptotagmin like 5

− 2.36

3.81E−06

 ENSG00000155850

SLC26A2

Solute carrier family 26 member 2

− 2.01

5.79E−06

 ENSG00000103489

XYLT1

Xylosyltransferase 1

− 1.88

1.15E−05

 ENSG00000203727

SAMD5

Sterile alpha motif domain containing 5

− 1.97

1.61E−05

 ENSG00000146938

NLGN4X

Neuroligin 4 X-linked

− 2.06

2.08E−05

 ENSG00000176055

MBLAC2

Metallo-beta-lactamase domain containing 2

− 3.08

3.93E−05

 ENSG00000073282

TP63

Tumor protein p63

− 3.57

4.30E−05

 ENSG00000232727

YWHAEP1

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon pseudogene 1

− 2.16

1.04E−04

 ENSG00000114019

AMOTL2

Angiomotin like 2

− 2.01

1.20E−04

 ENSG00000143971

ETAA1

ETAA1, ATR kinase activator

− 2.04

2.23E−04

 ENSG00000082482

KCNK2

Potassium two pore domain channel subfamily K member 2

− 1.67

2.40E−04

 ENSG00000225980

OR7E19P

Olfactory receptor family 7 subfamily E member 19 pseudogene

− 3.05

2.43E−04

 ENSG00000280798

LINC00294

Long intergenic non-protein coding RNA 294

− 1.78

4.11E−04

 ENSG00000138380

CARF

Calcium responsive transcription factor

− 2.40

5.01E−04

 ENSG00000143669

LYST

lysosomal trafficking regulator

− 1.56

6.21E−04

 ENSG00000250305

TRMT9B

tRNA methyltransferase 9B (putative)

− 2.14

7.52E−04

 ENSG00000104432

IL7

Interleukin 7

− 1.62

8.32E−04