Table 2. Differentially expressed genes in the Longissimus thoracis muscle of high- and low- residual feed intake Nelore steers.
| Gene symbol | Locus | FPKM mean in the LRFI, more efficient group | FPKM mean in the HRFI, less efficient group | FC | q-value |
|---|---|---|---|---|---|
| ACSM1 | 25:18,349,642–18,413,897 | 3.55 | 5.72 | 0.69 | 0.01 |
| ACTC1 | 10:30,361,774–30,367,052 | 38.09 | 215.97 | 2.50 | 0.01 |
| AGTPBP1 | 8:80,234,812–80,433,199 | 3.93 | 6.13 | 0.64 | 0.01 |
| ARID5B | 28:18,003,722–18,195,950 | 8.95 | 14.85 | 0.73 | 0.01 |
| ARRDC3 | 7:93,238,461–93,253,182 | 11.18 | 17.37 | 0.64 | 0.01 |
| ATF3 | 16:72,819,913–72,878,316 | 37.33 | 69.89 | 0.90 | 0.01 |
| B3GALTL | 12:29,659,763–29,776,394 | 2.58 | 469.34 | 7.51 | 0.01 |
| BDH1 | 1:72,572,762–72,610,397 | 1.81 | 4.29 | 1.25 | 0.01 |
| BLA-DQB | 23:25,855,144–25,863,045 | 18.93 | 11.68 | −0.70 | 0.01 |
| BTG2 | 16:889,144–894,202 | 28.67 | 39.98 | 0.48 | 0.04 |
| C3 | 7:18,989,626–19,025,593 | 1.08 | 0.38 | −1.51 | 0.01 |
| CASQ2 | 3:27,658,847–27,729,891 | 18.89 | 26.59 | 0.49 | 0.03 |
| CD109 | 9:13,421,006–13,556,277 | 3.24 | 4.63 | 0.52 | 0.01 |
| CD209 | 7:17,810,225–17,814,276 | 5.53 | 9.50 | 0.78 | 0.03 |
| CHRND | 2:120,974,969–120,982,375 | 3.81 | 9.52 | 1.32 | 0.01 |
| CISH | 22:50,320,098–50,325,618 | 9.66 | 6.026 | −0.68 | 0.01 |
| COL14A1 | 14:83,876,538–84,110,654 | 8.21 | 11.82 | 0.53 | 0.01 |
| COL6A6 | 1:153,321,010–153,494,877 | 1.80 | 2.74 | 0.61 | 0.01 |
| COQ10B | 2:86,410,716–86,427,939 | 10.36 | 17.46 | 0.75 | 0.01 |
| CYP1A1 | 21:34,340,289–34,351,607 | 8.57 | 5.79 | −0.57 | 0.01 |
| CYP1B1 | 11:20,490,140–20,499,187 | 0.73 | 1.42 | 0.95 | 0.04 |
| EBF1 | 7:72,393,224–72,804,822 | 5.59 | 7.78 | 0.48 | 0.04 |
| EFEMP1 | 11:38,338,736–38,408,331 | 14.28 | 19.66 | 0.46 | 0.03 |
| EGR1 | 7:51,438,703–51,442,530 | 23.47 | 39.95 | 0.77 | 0.01 |
| EIF4EBP1 | 27:32,951,593–32,973,439 | 60.84 | 43.39 | −0.49 | 0.05 |
| EMILIN2 | 24:37,496,209–37,556,462 | 2.80 | 4.07 | 0.54 | 0.02 |
| ENAH | 16:29,229,604–29,442,778 | 8.41 | 12.62 | 0.59 | 0.01 |
| F13A1 | 23:48,633,935–48,776,698 | 6.80 | 9.75 | 0.52 | 0.01 |
| FSTL1 | 1:65,742,625–65,802,423 | 53.10 | 77.77 | 0.55 | 0.04 |
| GAS7 | 19:29,665,966–29,876,650 | 3.17 | 4.67 | 0.56 | 0.02 |
| GFPT2 | 7:772,140–817,776 | 5.34 | 8.00 | 0.58 | 0.01 |
| GSTP1 | 29:46,087,141–46,090,009 | 99.65 | 72.21 | −0.46 | 0.02 |
| HOXC10 | 5:26,201,346–26,215,613 | 13.95 | 9.94 | −0.49 | 0.04 |
| IER5 | 16:63,677,268–63,691,626 | 12.94 | 18.76 | 0.54 | 0.01 |
| IFI6 | 2:126,246,575–126,250,174 | 11.55 | 19.93 | 0.79 | 0.03 |
| KERA | 5:20,995,310–21,003,085 | 1.96 | 3.87 | 0.98 | 0.01 |
| KIAA1551 | 5:78,299,287–78,326,541 | 2.73 | 3.79 | 0.48 | 0.05 |
| LIMK1 | 25:33,749,961–33,775,754 | 4.61 | 3.022 | −0.60 | 0.04 |
| LOC100300305 | 23:30,817,650–30,825,629 | 8.59 | 15.45 | 0.85 | 0.01 |
| LOC100335754 | 11:104,181,959–104,185,687 | 153.48 | 90.65 | −0.76 | 0.01 |
| LOC100336823 | 29:44,770,858–44,771,621 | 75.35 | 45.50 | −0.73 | 0.01 |
| LOC100848726 | 29:50,712,831–50,713,218 | 7453.97 | 151.88 | −5.62 | 0.01 |
| LOC100848909 | 6:92,504,246–92,544,085 | 172.60 | 0.52 | −8.39 | 0.01 |
| LOC782776 | 1:77,035,495–77,037,254 | 25.62 | 45.29 | 0.82 | 0.01 |
| LOC787803 | X:94,701,246–94,701,909 | 11.88 | 1.97 | −2.59 | 0.01 |
| LYVE1 | 15:42,678,143–42,693,086 | 6.48 | 9.93 | 0.62 | 0.01 |
| MDM4 | 16:2,065,963–2,106,826 | 3.82 | 5.62 | 0.56 | 0.05 |
| MEDAG | 12:30,016,965–30,040,051 | 12.83 | 17.77 | 0.47 | 0.04 |
| MPZ | 3:8,229,125–8,235,252 | 19.54 | 12.56 | −0.64 | 0.01 |
| MYC | 14:13,769,241–13,774,939 | 5.61 | 8.55 | 0.61 | 0.02 |
| MYL3 | 22:53,161,299–53,224,114 | 790.03 | 377.60 | −1.07 | 0.01 |
| NDUFS7 | 7:45,427,303–45,433,438 | 284.04 | 199.60 | −0.51 | 0.04 |
| NIN | 10:43,637,003–43,745,262 | 1.74 | 2.46 | 0.50 | 0.04 |
| NOV | 14:47,005,556–47,014,101 | 14.72 | 23.45 | 0.67 | 0.01 |
| NR4A2 | 2:39,944,984–40,017,777 | 4.94 | 8.51 | 0.78 | 0.01 |
| OTUD1 | 13:24,655,213–24,658,469 | 104.97 | 172.28 | 0.71 | 0.02 |
| PARP2 | 10:26,799,838–26,814,591 | 9.40 | 5.11 | −0.88 | 0.01 |
| PI15 | 14:40,275,630–40,313,055 | 0.94 | 2.13 | 1.18 | 0.01 |
| PKHD1L1 | 14:57,040,806–57,216,685 | 0.43 | 0.76 | 0.84 | 0.01 |
| RIF1 | 2:44,756,972–44,819,250 | 3.36 | 4.66 | 0.47 | 0.01 |
| RN18S1 | 25:32,428,075–32,430,097 | 20102.70 | 835.18 | −4.59 | 0.01 |
| RN28S1 | 3:53,470,477–53,472,889 | 8751.13 | 351.13 | −4.64 | 0.01 |
| RN28S1 | 3:35,428,057–35,862,958 | 9997.71 | 376.81 | −4.73 | 0.01 |
| RN5-8S1 | 25:32,467,531–32,467,688 | 32282.90 | 293.23 | −6.78 | 0.01 |
| RSPO2 | 14:58,537,058–58,709,246 | 0.29 | 1.51 | 2.38 | 0.01 |
| SBK2 | 18:62,434,331–62,439,412 | 0.83 | 3.22 | 1.95 | 0.01 |
| SLC26A2 | 7:63,280,898–63,303,387 | 0.64 | 1.09 | 0.77 | 0.01 |
| TGFBR3 | 3:51,660,730–51,870,069 | 13.65 | 19.77 | 0.53 | 0.05 |
| THBS3 | 3:15,470,267–15,480,514 | 1.60 | 2.73 | 0.77 | 0.02 |
| TIPARP | 1:111,829,353–111,857,046 | 4.79 | 7.58 | 0.66 | 0.01 |
| TNMD | X:50,951,554–50,973,156 | 1.75 | 5.10 | 1.54 | 0.01 |
| UCHL1 | 6:61,785,263–61,807,737 | 9.82 | 5.97 | −0.72 | 0.01 |
| WDR74 | 29:41,838,790–41,846,756 | 13.40 | 8.95 | −0.58 | 0.01 |
LRFI = Low Residual Feed Intake; HRFI = High Residual Feed Intake; FC = log2-fold change; q-value = FDR-adjusted p-value.