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 |