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Table 4 Top 50 annotated genes with decreased methylation, ranked by log2-fold change

From: Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq

Rank Symbol Gene name Log2 fold change (TRAMP/WT) Location Type(s) Methylation region
1 Rrbp1 Ribosome-binding protein 1 − 5.824 Cytoplasm Transporter Body
2 CISD2 CDGSH iron sulfur domain 2 − 4.373 Cytoplasm Other Downstream
3 NR4A1 Nuclear receptor subfamily 4, group A, member 1 − 4.324 Nucleus Ligand-dependent nuclear receptor Body
4 LCMT1 Leucine carboxyl methyltransferase 1 − 4.051 Cytoplasm Enzyme Body
5 XRCC6BP1 XRCC6 binding protein 1 − 3.990 Other Kinase Downstream
6 TTR Transthyretin − 3.926 Extracellular space Transporter Promoter
7 ZNF536 Zinc finger protein 536 − 3.859 Other Other Downstream
8 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived) − 3.788 Plasma membrane Other Body
9 TNRC18 Trinucleotide repeat containing 18 − 3.788 Other Other Body
10 FOXL1 Forkhead box L1 − 3.714 Nucleus Transcription regulator Downstream
11 ZMAT4 Zinc finger, matrin-type 4 − 3.714 Nucleus Other Promoter
12 ABCC2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 − 3.636 Plasma membrane Transporter Body
13 AMFR Autocrine motility factor receptor, E3 ubiquitin protein ligase − 3.636 Plasma membrane Transmembrane receptor Downstream
14 ARSK Arylsulfatase family, member K − 3.636 Extracellular space enzyme Body
15 GRM3 Glutamate receptor, metabotropic 3 − 3.636 Plasma membrane G-protein coupled receptor Promoter
16 HTR1F 5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled − 3.636 Plasma membrane G-protein coupled receptor Body
17 CC2D2A Coiled-coil and C2 domain containing 2A − 3.554 Other Other Promoter
18 CSMD1 CUB and Sushi multiple domains 1 − 3.554 Plasma membrane Other Body
19 HIBCH 3-Hydroxyisobutyryl-CoA hydrolase − 3.554 Cytoplasm Enzyme Body
20 NMT2 N-Myristoyltransferase 2 − 3.554 Cytoplasm Enzyme Promoter
21 PCDH20 Protocadherin 20 − 3.554 Other Other Promoter
22 PDCD1 Programmed cell death 1 − 3.554 Plasma membrane Phosphatase Promoter
23 QRFP Pyroglutamylated RFamide peptide − 3.554 Extracellular space Other Downstream
24 REG3G Regenerating islet-derived 3 gamma − 3.554 Extracellular space Other Downstream
25 TLR4 Toll-like receptor 4 − 3.554 Plasma membrane Transmembrane receptor Downstream
26 TNRC6B Trinucleotide repeat containing 6B − 3.554 Other Other Body
27 CCR3 Chemokine (C–C motif) receptor 3 − 3.466 Plasma membrane G-protein coupled receptor Promoter
28 Cngb1 Cyclic nucleotide gated channel beta 1 − 3.466 Other Other Body
29 CNTNAP5 Contactin associated protein-like 5 − 3.466 Other Other Body
30 Cox7c Cytochrome c oxidase subunit VIIc − 3.466 Cytoplasm Other Promoter
31 EIF4EBP1 Eukaryotic translation initiation Factor 4E binding protein 1 − 3.466 Cytoplasm Translation regulator Downstream
32 FGF10 Fibroblast growth factor 10 − 3.466 Extracellular space Growth factor Downstream
33 GNAI1 Guanine nucleotide-binding protein (G protein), alpha inhibiting activity polypeptide 1 − 3.466 Plasma membrane Enzyme Promoter
34 Ins1 Insulin I − 3.466 Extracellular space Other Promoter
35 ITGA8 Integrin, alpha 8 − 3.466 Plasma membrane Other Body
36 JAG1 Jagged 1 − 3.466 Extracellular space Growth factor Promoter
37 Pcdh10 Protocadherin 10 − 3.466 Other Other Promoter
38 PPP1R17 Protein phosphatase 1, regulatory subunit 17 − 3.466 Cytoplasm Other Downstream
39 Serbp1 Serpine1 mRNA-binding protein 1 − 3.466 Cytoplasm Other Promoter
40 Wasl Wiskott-Aldrich syndrome-like (human) − 3.466 Cytoplasm Other Promoter
41 ABAT 4-Aminobutyrate aminotransferase − 3.373 Cytoplasm Enzyme Body
42 ANKMY2 Ankyrin repeat and MYND domain containing 2 − 3.373 Plasma membrane Other Downstream
43 Card11 Caspase recruitment domain family, member 11 − 3.373 Other Other Body
44 CDK5R1 Cyclin-dependent kinase 5, regulatory subunit 1 (p35) − 3.373 Nucleus Kinase Downstream
45 DACH1 Dachshund family transcription factor 1 − 3.373 Nucleus Transcription regulator Downstream
46 FGGY FGGY carbohydrate kinase domain containing − 3.373 Other Other Body
47 GADD45G Growth arrest and DNA-damage-inducible, gamma − 3.373 Nucleus Other Downstream
48 GLRB Glycine receptor, beta − 3.373 Plasma membrane Ion channel Body
49 LRRTM1 Leucine-rich repeat transmembrane neuronal 1 − 3.373 Plasma membrane Other Downstream
50 NEDD4L Neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase − 3.373 Cytoplasm Enzyme Body