Table 4.
Comparison between DEGs observed in the aging lens fibers with those previously found to exhibit differential histone H3K4 trimethylation in the aging lens (Zheng et al., 2015). Italicized genes represent those where the expected direction of change in mRNA levels and H3K4 trimethylation is discordant
| SYMBOL | DESCRIPTION | Young fibers FPKM | Aged fibers FPKM | Aged fibers versus Young fibers fold change expression | Aged fibers versus Young fibers FDR expression | Aged fibers versus Young lens fold change methylation | Aged fibers versus Young lens methylation FDR |
|---|---|---|---|---|---|---|---|
| Igf2bp2 | insulin-like growth factor 2 mRNA binding protein 2 | 2.0 | 0.0 | −1042.2 | 4.7E-29 | −14.5 | 4.0E-67 |
| Eva1a | eva-1 homolog A (C. elegans) | 15.6 | 0.7 | −22.6 | 4.0E-19 | −1.6 | 4.6E-02 |
| B230312C02Rik | RIKEN cDNA B230312C02 gene | 6.4 | 0.6 | −10.7 | 2.5E-12 | −2.0 | 3.1E-02 |
| Snx22 | sorting nexin 22 | 76.0 | 8.0 | −9.5 | 1.1E-08 | −1.7 | 2.1E-03 |
| Crygn | crystallin, gamma N | 157.4 | 19.9 | −8.0 | 3.9E-15 | −5.3 | 4.1E-04 |
| 1700101I11Rik | RIKEN cDNA 1700101I11 gene | 8.2 | 1.1 | −7.8 | 1.2E-08 | −1.6 | 1.6E-03 |
| Rasgrp1 | RAS guanyl releasing protein 1 | 2.5 | 0.4 | −6.6 | 1.8E-03 | −1.8 | 4.9E-02 |
| Stxbp6 | syntaxin binding protein 6 (amisyn) | 5.2 | 0.9 | −6.0 | 4.3E-11 | −2.1 | 1.6E-03 |
| Zfyve28 | zinc finger, FYVE domain containing 28 | 11.0 | 1.8 | −5.9 | 3.7E-09 | −2.8 | 1.9E-07 |
| Lhfp | lipoma HMGIC fusion partner | 3.4 | 0.6 | −5.5 | 4.7E-04 | −1.6 | 2.1E-02 |
| Lgi2 | leucine-rich repeat LGI family, member 2 | 5.6 | 1.1 | −5.2 | 4.2E-22 | −2.1 | 4.8E-03 |
| Crybb1 | crystallin, beta B1 | 10608.6 | 2162.6 | −4.9 | 1.1E-10 | 1.6 | 1.8E-05 |
| Wnk2 | WNK lysine deficient protein kinase 2 | 13.2 | 2.8 | −4.8 | 3.2E-27 | −1.8 | 1.1E-04 |
| Stambpl1 | STAM binding protein like 1 | 17.4 | 3.9 | −4.4 | 9.7E-04 | −1.7 | 1.2E-03 |
| Gck | glucokinase | 4.2 | 1.0 | −4.3 | 6.0E-04 | −2.5 | 2.4E-05 |
| Gng2 | guanine nucleotide binding protein (G protein), gamma 2 | 9.8 | 2.5 | −3.9 | 2.5E-17 | −1.9 | 1.6E-02 |
| Slc7a5 | solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 | 19.0 | 4.9 | −3.9 | 8.8E-24 | −2.3 | 2.4E-11 |
| Chchd7 | coiled-coil-helix-coiled-coil-helix domain containing 7 | 13.7 | 3.6 | −3.8 | 4.1E-16 | −1.9 | 9.5E-11 |
| Galnt14 | polypeptide N-acetylgalactosaminyltransferase 14 | 3.7 | 1.0 | −3.7 | 3.1E-04 | −3.0 | 1.4E-02 |
| Gabarapl1 | gamma-aminobutyric acid (GABA) A receptor-associated protein-like 1 | 87.3 | 26.5 | −3.3 | 3.0E-27 | −1.6 | 1.6E-03 |
| Itpk1 | inositol 1,3,4-triphosphate 5/6 kinase | 16.0 | 5.0 | −3.2 | 6.2E-13 | −1.6 | 3.2E-04 |
| Cryaa | crystallin, alpha A | 57208.0 | 18646.8 | −3.1 | 2.1E-12 | 1.5 | 5.9E-03 |
| Ube2o | ubiquitin-conjugating enzyme E2O | 106.9 | 37.7 | −2.8 | 3.5E-19 | −1.7 | 1.6E-04 |
| Timeless | timeless circadian clock 1 | 14.2 | 5.0 | −2.8 | 4.3E-07 | 2.0 | 1.0E-02 |
| Fxyd1 | FXYD domain-containing ion transport regulator 1 | 43.7 | 16.6 | −2.6 | 2.4E-16 | 2.1 | 2.4E-02 |
| S100a6 | S100 calcium binding protein A6 (calcyclin) | 255.2 | 115.5 | −2.2 | 4.0E-17 | 3.3 | 1.6E-34 |
| Fam210b | family with sequence similarity 210, member B | 6.7 | 3.1 | −2.2 | 7.4E-06 | −1.5 | 2.9E-03 |
| D630045J12Rik | RIKEN cDNA D630045J12 gene | 7.9 | 3.6 | −2.2 | 2.9E-08 | −1.5 | 7.2E-03 |
| Neat1 | nuclear paraspeckle assembly transcript 1 | 2.6 | 5.8 | 2.2 | 1.0E-07 | 1.8 | 6.8E-12 |
| Jup | junction plakoglobin | 3.5 | 8.2 | 2.4 | 7.1E-10 | 2.8 | 2.5E-12 |
| S100a13 | S100 calcium binding protein A13 | 1.6 | 4.4 | 2.8 | 3.4E-02 | 2.9 | 9.9E-05 |
| Scarf2 | scavenger receptor class F, member 2 | 1.2 | 3.4 | 2.9 | 8.1E-04 | 2.1 | 7.0E-05 |
| Tjp2 | tight junction protein 2 | 1.4 | 4.2 | 3.0 | 1.7E-16 | 1.6 | 1.5E-03 |
| Scel | sciellin | 2.3 | 7.9 | 3.5 | 4.3E-06 | 1.7 | 6.1E-04 |
| Rtn1 | reticulon 1 | 0.9 | 3.2 | 3.5 | 7.1E-10 | 4.2 | 1.2E-19 |
| Cyp26a1 | cytochrome P450, family 26, subfamily a, polypeptide 1 | 3.4 | 12.0 | 3.5 | 7.4E-06 | 2.1 | 7.3E-09 |
| Phlda3 | pleckstrin homology like domain, family A, member 3 | 6.9 | 25.3 | 3.6 | 7.1E-09 | 2.5 | 4.3E-14 |
| E130102H24Rik | RIKEN cDNA E130102H24 gene | 1.1 | 4.1 | 3.8 | 2.9E-02 | 1.6 | 5.5E-05 |
| Serpinb6b | serine (or cysteine) peptidase inhibitor, clade B, member 6b | 20.5 | 77.3 | 3.8 | 1.6E-28 | 4.5 | 3.9E-12 |
| Dmpk | dystrophia myotonica-protein kinase | 3.8 | 15.7 | 4.2 | 1.8E-24 | 2.3 | 1.9E-04 |
| Esyt3 | extended synaptotagmin-like protein 3 | 0.8 | 3.3 | 4.3 | 8.0E-19 | 1.5 | 4.1E-04 |
| Ephx1 | epoxide hydrolase 1, microsomal | 9.4 | 44.4 | 4.7 | 1.3E-32 | 2.1 | 4.1E-04 |
| Trim47 | tripartite motif-containing 47 | 1.0 | 4.9 | 4.8 | 1.6E-10 | 3.4 | 1.2E-18 |
| Pdpn | podoplanin | 2.7 | 15.2 | 5.6 | 2.6E-09 | 1.7 | 1.6E-05 |
| R3hdml | R3H domain containing-like | 7.3 | 41.4 | 5.6 | 5.0E-05 | 2.1 | 7.0E-07 |
| Cd9 | CD9 antigen | 1.3 | 7.4 | 5.8 | 3.5E-18 | 2.5 | 2.9E-10 |
| Cdkn2b | cyclin dependent kinase inhibitor 2B | 3.7 | 23.9 | 6.4 | 5.8E-13 | 2.3 | 5.5E-06 |
| Cnksr1 | connector enhancer of kinase suppressor of Ras 1 | 0.4 | 2.7 | 6.8 | 8.7E-09 | 4.6 | 2.3E-09 |
| Hmgcs2 | 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 | 2.0 | 14.9 | 7.3 | 1.3E-03 | 5.9 | 4.0E-10 |
| Ddit4l | DNA-damage-inducible transcript 4-like | 0.5 | 3.7 | 7.5 | 3.2E-07 | 2.0 | 1.3E-03 |
| Ntn4 | netrin 4 | 0.7 | 6.0 | 8.8 | 2.3E-26 | 2.4 | 4.2E-11 |
| Igfbp5 | insulin-like growth factor binding protein 5 | 0.6 | 5.8 | 10.2 | 4.4E-06 | −1.9 | 2.2E-03 |
| Ifi27 | interferon, alpha-inducible protein 27 | 0.1 | 2.6 | 20.3 | 5.4E-11 | 2.2 | 1.2E-04 |
| Ndufa4l2 | Ndufa4, mitochondrial complex associated like 2 | 0.3 | 6.8 | 21.0 | 3.3E-07 | 3.9 | 5.1E-08 |