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Table 2 Annotations for the 35 FDR significant CpGs (adjusted p values < 0.05) for cisplatin-based chemotherapy (CBCT) model

From: Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome

CpG name

Gene namea

FDRb

Bonfc

Function of the gene product

Disease/Trait associationd

cg07677157

RP11-221N13.4

9.56E-15

9.56E-15

  

cg08057120

 

7.78E-12

1.56E-11

  

cg26408927

CACNA1D

2.26E-10

6.79E-10

Mediate the entry of calcium ions into excitable cells. Involved in a variety of calcium-dependent processes. Regulates intracellular processes such as contraction, secretion, neurotransmission and other gene expression

Sinoatrial node dysfunction and deafness. Hypertension. Body mass index. Insulin resistance/response. Systolic blood pressure. Diastolic blood pressure. Visceral adipose tissue/subcutaneous adipose tissue ratio. Type 2 diabetes

cg27487222

 

7.37E-07

2.95E-06

  

cg11031221

LINC00511

1.56E-06

7.78E-06

A long non-protein coding RNA, involved in the regulation of gene expression during tumor progression

 

cg22688137

 

6.01E-05

< 0.001

  

cg24833462

AC023672.2

< 0.001

< 0.001

  

cg20063141

ONECUT2/

AC090340.1

< 0.001

0.004

This gene encodes a member of the one cut family of transcription factors, which are characterized by a cut domain and an atypical homeodomain

 

cg08889373

ACOT7/RP1-202O8.3

0.001

0.009

Protein hydrolyzes the CoA thioester of palmitoyl-CoA and other long-chain fatty acids

Type 2 diabetes. Atherosclerosis

cg14792781

GRHL1

0.002

0.016

Is a transcription factor necessary during development

Cancer. Type 1 diabetes

cg14634473

 

0.002

0.021

  

cg21940081

IMP4

0.003

0.037

Part of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP) complex. Responsible for early cleavage steps of pre-18S ribosomal RNA processing

 

cg03877706

NCAM2

0.003

0.041

Belongs to the immunoglobulin superfamily. May play important roles in selective fasciculation and zone-to-zone projection of the primary olfactory axons

Obesity. Visceral fat

cg00303773

TOM1L2

0.005

0.070

Participate in vesicular trafficking. Play a role in endosomal sorting

Body mass. Type 2 diabetes

cg10113471

 

0.005

0.069

  

cg23304747

PITPNM2

0.008

0.123

Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro). Binds calcium ions

 

cg14972510

BAG4

0.010

0.167

Inhibits the chaperone activity of HSP70/HSC70. Prevents constitutive TNFRSF1A signaling. Negative regulator of PRKN translocation to damaged mitochondria

 

cg26561082

DIP2C

0.011

0.197

The protein shares strong similarity with a Drosophila protein which interacts with the transcription factor disco and is expressed in the nervous system

Blood metabolite levels

cg24869056

HPS1

0.012

0.235

Play a role in organelle biogenesis associated with melanosomes, platelet dense granules and lysosomes

Obesity-related traits

cg14629524

KDM3B

0.020

0.401

Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code

 

cg04156896

MFSD2A

0.021

0.459

Transmembrane protein and sodium-dependent lysophosphatidylcholine transporter involved in the establishment of the blood-brain barrier

 

cg27367992

ST6GAL1

0.021

0.451

Catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates

Type 2 diabetes

cg08343240

AC008703.1

0.024

0.573

RNA gene

 

cg27545041

 

0.024

0.567

An important paralog of this gene is INTS6 / RNA Gene and is affiliated with the non-coding RNA class

 

cg04046944

CACNA1S

0.025

0.614

This gene encodes one of the five subunits of the slowly inactivating L-type voltage-dependent calcium channel in skeletal muscle cells

 

cg06225648

 

0.025

0.651

  

cg12381697

CCM2

0.028

0.751

  

cg13207339

PARK2

0.030

0.849

A component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrate proteins for proteasomal degradation

Metabolite levels. Body mass index. Aging

cg22345432

PXN/

PXN-AS1

0.033

0.972

Involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion)/RNA Gene and is affiliated with the non-coding RNA class

 

cg17158941

C7orf50/AC073957.15

0.040

1

Chromosome 7 Open Reading Frame 50

C-reactive protein levels or total cholesterol levels

cg03289031

ZNF629

0.040

1

  

cg26540402

PRF1

0.040

1

Plays a key role in secretory granule-dependent cell death and in defense against virus infected or neoplastic cells

 

cg16657582

 

0.043

1

  

cg21902759

RAB40B

0.043

1

Substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins

 

cg19377056

ARHGAP39

0.049

1

  
  1. aUCSC gene name
  2. bFDR - CBCT False Discovery Rate significance (p < 0.05)
  3. cBonf - CBCT Bonferroni significance (p < 0.05)
  4. dSelected from GeneToFunction database (human only) and Gene Cards disease associations