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Table 2 Identification of up regulated genes identified in E1A expressing quiescent cells and required for DNA repair, checkpoint controls, and the DNA damage response.

From: The dynamics of E1A in regulating networks and canonical pathways in quiescent cells

Accession

Gene Symbol

Description

E2F4 binding 1,2

Zcut

glog(FC)

  

DNA repair processes: homologous recombination, mismatch/excision repair, and non-homologous end-joining

   

NM_007499.1

ATM

Ataxia telangiectasia mutated

+

7.498

0.585

NM_007550

BLM

Bloom syndrome, RecQ helicase-like

+

20.559

1.529

NM_009764.2

BRCA1

Breast cancer 1, early onset

-

4.757

0.381

NM_009765.1

BRCA2

Breast cancer 2, early onset

-

12.234

0.927

NM_007691.2 NM_009863.1

CHEK1 CDC7

CHK1 checkpoint homolog (S. Pombe) Cell division cycle 7 homolog (S. cerevisiae)

+ +

3.202 17.694

0.261 1.321

NM_028119.2

DDB2

Damage-specific DNA binding protein 2, 48 kDa

+

9.204

0.709

NM_177752.2

EME1

Essential meiotic endonuclease 1 homolog 1 (S. pombe)

-

2.820

0.232

NM_001033244.1

FANCD2

Fanconi anemia, complementation group D2

+

9.508

0.730

NM_007999.2

FEN1

Flap structure-specific endonucleae 1

+

8.577

1.957

NM_010436.2

H2AFX

H2A histone family, member X

+

4.634

1.095

NM_010715.1

LIG1

Ligase 1, DNA, ATP-dependent

+

18.060

1.348

NM_026810.1

MLH1

MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)

+

2.794

0.230

NM_018736.2

MRE11A

MRE11 meiotic recombination 11 homolog A (S. cerevisiae)

-

5.432

0.432

NM_008628.1

MSH2

MutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)

+

3.107

0.254

NM_010830.1

MSH6

MutS homolog 6 (E.coli)

-

13.241

1.000

NM_013752

NBN

Nibrin

-

8.326

0.645

NM_009632.2

PARP2

Poly (ADP-ribose) polymerase 2

+

7.656

0.596

NM_011045.1

PCNA

Proliferating cell nuclear antigen

+

10.999

0.838

NM_008886.1

PMS2

PMS2 postmeiotic segregation increased 2 (S. cerevisiae)

-

8.409

0.651

NM_011131.2

POLD1

Polymerase (DNA directed) delta 1, catalytic subunit 125 kDa

+

7.744

0.603

NM_030715.2 NM_008949.2

POLH PSMC3IP

Polymerase (DNA directed), eta PSMC3 interacting protein

- +

3.448 17.496

0.825 1.307

NM_013917.1 NM_021385.1

PTTG1 RAD18

Pituitary tumor-transforming 1 RAD18 homolog (S. cerevisiae)

+ +

7.190 7.629

0.562 0.594

NM_009012.1

RAD50

RAD50 homolog (S. cerevisiae)

+

4.064

0.328

NM_011234.2

RAD51

RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)

+

12.514

0.947

NM_009013.1

RAD51AP1

RAD51 associated protein 1

+

9.638

0.740

NM_009015.2

RAD54L

RAD54-like (S. cerevisiae)

+

9.320

2.115

NM_026653.1

RPA1

Replication protein A1, 70 kDa

-

9.177

0.707

NM_011237.1

RAD9A

RAD9A homolog A

-

4.501

0.361

NM_023042.1

RECQL

RecQ protein-like (DNA helicase Q1-like)

+

5.724

0.125

NM_021419.1

RNF8

Ringfinger protein 8

+

2.663

0.222

NM_011677.1

UNG

Uracil-DNA glycosylase

+

4.901

0.475

NM_133786.3 NM_153808.1

SMC4L1 SMC5L1

Structural maintenance of chromosomes four-like 1 Structural maintenance of chromosomes five-like 1

- -

4.290 10.047

0.345 0.769

XM_127444.3 NM_010247.1

TRIP13 XRCC6

Thyroid hormone receptor interactor 13 X-ray repair complementing defective repair in Chinese hamster

+ -

3.630 3.039

0.294 0.732

Accession

Gene Symbol

Description

E2F4 binding 1,2

Zcut

glog(FC)

  

DNA damage response

   

NM_007499.1

ATM

Ataxia telangiectasia mutated

+

7.498

0.585

NM_009764.2

BRCA1

Breast cancer 1, early onset

-

4.757

0.381

NM_009765.1

BRCA2

Breast cancer 2, early onset

-

12.234

0.927

NM_007691.2

CHEK1

CHK1 checkpoint homolog (S. Pombe)

+

3.202

0.261

NM_001033244.1

FANCD2

Fanconi anemia, complementation group D2

+

9.508

0.730

NM_008316.2

HUS1

HUS1 checkpoint homolog (S. pombe)

-

4.438

0.357

NM_010774.1

MBD4

Methyl-CpG binding domain protein 4

-

8.816

0.681

NM_008583.1

MEN1

Multiple endocrine neoplasia 1

?

4.995

0.399

NM_026810.1

MLH1

MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)

+

2.794

0.230

NM_008628.1

MSH2

MutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)

+

3.107

0.254

NM_010830.1

MSH6

Muts homolog 6 (E. coli)

-

13.241

1.000

NM_008884.2

PML

Promyelocytic leukemia

-

3.155

0.257

NM_011237.1

RAD9A

RAD9 homolog A (S. pombe)

-

4.501

0.361

NM_011234.2

RAD51

RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)

+

12.514

0.947

NM_009015.2

RAD54L

RAD54-like (S. cerevisiae)

+

9.320

2.115

NM_026653.1

RPA1

Replicaton protein A1, 70 kDa

+

9.177

0.707

NM_011623.1

TOP2A

Topoisomerase (DNA) 11 alpha 170 kDa

+

8.224

1.880

NM_011640.1

TP53

Tumor protein p53

-

6.333

0.499

NM_010247.1

XRCC6

X-ray repair complementing defective repair in Chinese hamster

-

3.039

0.732

Accession

Gene Symbol

Description

E2F4 binding 1,2

Zcut

glog(FC)

  

DNA replication checkpoints and checkpoint control

   

NM_007499.1

ATM

Ataxia telangiectasia mutated

+

7.498

0.585

NM_026014.3

CDT1

Chromatin licensing and DNA replication factor 1

-

4.137

0.983

NM_007691.2 NM_008316.2

CHEK1 HUS1

CHK1 checkpoint homolog (S. Pombe) HUS1, checkpoint homolog (S. pombe)

+ +

3.202 4.438

0.261 0.357

NM_008583.1

MEN1

Multiple endocrine neoplasia 1

-

4.995

0.399

NM_008628.1

MSH2

MutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)

+

3.107

0.254

NM_134092.2

MTBP

Mdm2, transformed 3T3 cell double minute 2

+

9.084

0.700

NM_011237.1

RAD9A

RAD9 homolog A (S. pombe)

+

4.501

0.361

NM_011640.1

TP53

Tumor protein p53

-

6.333

0.499

  1. 1,2 Data for the binding of E2F4 was obtained from Ren et al. 2002 (superscript 1) and Xu et al. 2007 (superscript 2). Generalized-log-fold change values (glog(FC)) represent the corresponding magnitude of regulation of the selected genes.