Table 3 SAM genes that were upregulated in cell lines compared to tumors in all the 6 tissues considered in the study (CL - T).

ATP5B

ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide

Oxidative phosphorylation, ATP synthesis

ATP5G3

ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C3 (subunit 9)

ATP synthesis, Oxidative phosphorylation

C1QBP

complement component 1, q subcomponent binding protein

(Immune Response)

CBX3

chromobox homolog 3 (HP1 gamma homolog, Drosophila)

N/A

CCNB1

cyclin B1

Cell cycle

CCT5

chaperonin containing TCP1, subunit 5 (epsilon)

N/A

CDC20

CDC20 cell division cycle 20 homolog (S. cerevisiae)

Ubiquitin mediated proteolysis, Cell cycle

CDKN3

cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase)

N/A

CHAF1A

chromatin assembly factor 1, subunit A (p150)

N/A

CKAP1

cytoskeleton associated protein 1

N/A

CKS1B

CDC28 protein kinase regulatory subunit 1B

N/A

CKS2

CDC28 protein kinase regulatory subunit 2

N/A

COX8A

cytochrome c oxidase subunit 8A (ubiquitous)

Oxidative phosphorylation

CYC1

cytochrome c-1

Oxidative phosphorylation

DNMT1

DNA (cytosine-5-)-methyltransferase 1

Methionine metabolism

DYNLL1

dynein, light chain, LC8-type 1

N/A

EBNA1BP2

EBNA1 binding protein 2

N/A

HMGB2

high-mobility group box 2

N/A

KIAA0101

KIAA0101

N/A

KIF2C

kinesin family member 2C

N/A

LMNB2

lamin B2

Cell communication

MCM3

MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)

Cell cycle

MCM4

MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)

Cell cycle

MCM7

MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)

Cell cycle

MRPL12

mitochondrial ribosomal protein L12

N/A

NDUFS8

NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase)

Oxidative phosphorylation

PAICS

phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase

Purine metabolism

PCNA

proliferating cell nuclear antigen

Cell cycle

POLR2G

polymerase (RNA) II (DNA directed) polypeptide G

Purine metabolism, RNA polymerase, Pyrimidine metabolism

PRMT1

protein arginine methyltransferase 1

Selenoamino acid metabolism, Nitrobenzene degradation, Aminophosphonate metabolism, Tryptophan metabolism, Histidine metabolism, Androgen and estrogen metabolism, Tyrosine metabolism

PSMA1

proteasome (prosome, macropain) subunit, alpha type, 1

Proteasome

PSMB2

proteasome (prosome, macropain) subunit, beta type, 2

Proteasome

PSMB5

proteasome (prosome, macropain) subunit, beta type, 5

Proteasome

PSMB6

proteasome (prosome, macropain) subunit, beta type, 6

Proteasome

PSMD14

proteasome (prosome, macropain) 26S subunit, non-ATPase, 14

Proteasome

RANBP1

RAN binding protein 1

N/A

SFRS9

splicing factor, arginine/serine-rich 9

N/A

SNRPA

small nuclear ribonucleoprotein polypeptide A

N/A

SNRPB

small nuclear ribonucleoprotein polypeptides B and B1

N/A

SNRPC

small nuclear ribonucleoprotein polypeptide C

N/A

SNRPD2

small nuclear ribonucleoprotein D2 polypeptide 16.5kDa

N/A

SNRPD3

small nuclear ribonucleoprotein D3 polypeptide 18kDa

N/A

SNRPE

small nuclear ribonucleoprotein polypeptide E

N/A

SNRPF

small nuclear ribonucleoprotein polypeptide F

N/A

SNRPG

small nuclear ribonucleoprotein polypeptide G

N/A

TCEB1

transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)

Ubiquitin mediated proteolysis

TUBG1

tubulin, gamma 1

N/A

TXNRD1

thioredoxin reductase 1

Pyrimidine metabolism

TYMS

thymidylate synthetase

Pyrimidine metabolism, One carbon pool by folate

UBE2C

ubiquitin-conjugating enzyme E2C

Ubiquitin mediated proteolysis

UBE2S

ubiquitin-conjugating enzyme E2S

N/A