Table 2 Differentially expressed genes in the longissimus thoracis muscle of Nelore cattle divergent for intramuscular fat content phenotypes
From: Prediction of hub genes associated with intramuscular fat content in Nelore cattle
Gene | Locus | HIF (μ) | LIF (μ) | Fold change (log2)* | q value |
|---|---|---|---|---|---|
CDS1 | 6:101195739–101,273,209 | 0.56 | 1.92 | 1.79 | 0.02 |
TNC | 8:105965489–106,067,896 | 0.71 | 1.83 | 1.37 | 0.01 |
BARX2 | 29:33240583–33,256,128 | 1.49 | 3.60 | 1.28 | 0.04 |
EGR1 | 7:51438971–51,441,815 | 12.59 | 30.35 | 1.27 | 0.01 |
CCL2 | 19:16232955–16,234,822 | 9.64 | 21.62 | 1.16 | 0.01 |
MXRA5 | X:138875004–138,904,034 | 1.06 | 2.20 | 1.06 | 0.01 |
PCDH12 | 7:54685624–54,703,271 | 1.10 | 2.18 | 0.99 | 0.01 |
SLC22A4 | 7:23382631–23,425,462 | 3.93 | 7.81 | 0.99 | 0.04 |
SLC2A3 | 5:101896620–101,909,565 | 4.74 | 9.39 | 0.99 | 0.01 |
APLNR | 15:81734844–81,738,412 | 1.37 | 2.68 | 0.96 | 0.01 |
FSCN1 | 25:39292718–39,302,192 | 4.08 | 7.02 | 0.78 | 0.01 |
COL18A1 | 1:146989202–147,041,015 | 2.88 | 4.90 | 0.77 | 0.01 |
CLDN5 | 17:74749249–74,750,524 | 14.81 | 24.51 | 0.73 | 0.01 |
CD93 | 13:42244261–42,247,908 | 6.31 | 10.10 | 0.68 | 0.01 |
MCAM | 15:30414471–30,422,213 | 5.15 | 8.12 | 0.66 | 0.04 |
DLL4 | 10:36577284–36,586,360 | 2.68 | 4.21 | 0.65 | 0.04 |
BOLA | 23:28502516–28,506,343 | 41.94 | 65.42 | 0.64 | 0.01 |
IER2 | 7:13543658–13,548,059 | 4.94 | 7.62 | 0.63 | 0.05 |
IER3 | 23:28088454–28,089,726 | 10.11 | 15.49 | 0.62 | 0.04 |
PLXND1 | 22:56776197–56,825,067 | 2.38 | 3.58 | 0.59 | 0.01 |
PPP1R3B | 27:24314781–24,323,720 | 13.34 | 19.54 | 0.55 | 0.04 |
NFKBIA | 21:46065545–46,068,942 | 32.35 | 21.85 | −0.57 | 0.04 |
CRISPLD2 | 18:10985131–11,050,908 | 13.29 | 8.90 | −0.58 | 0.04 |
ANKRD52 | 5:57399491–57,415,909 | 9.99 | 6.62 | −0.59 | 0.01 |
MED25 | 18:56632972–56,645,624 | 13.37 | 8.79 | −0.61 | 0.04 |
NT5C2 | 26:23983197–24,080,607 | 33.01 | 21.57 | −0.61 | 0.04 |
FOXO1 | 12:21915289–22,009,079 | 11.38 | 7.37 | −0.63 | 0.01 |
PMP22 | 19:33357138–33,386,333 | 36.62 | 23.67 | −0.63 | 0.01 |
RPS6KA3 | X:130145854–130,305,125 | 90.58 | 58.17 | −0.64 | 0.01 |
GADD45A | 3:77972151–77,975,240 | 44.72 | 28.68 | −0.64 | 0.01 |
SFMBT1 | 22:48444152–48,549,526 | 6.77 | 4.33 | −0.65 | 0.04 |
LOC786565 | 7:54392624–54,437,291 | 39.05 | 24.83 | −0.65 | 0.01 |
CIPC | 10:89365865–89,381,544 | 55.74 | 35.31 | −0.66 | 0.02 |
LOC782855 | 6:81188550–81,188,972 | 114.47 | 72.10 | −0.67 | 0.02 |
LOC104973907 | 13:78185912–78,193,935 | 6.04 | 3.78 | −0.68 | 0.01 |
DNAJA1 | 8:76107881–76,117,637 | 49.92 | 31.06 | −0.68 | 0.01 |
NFIL3 | 8:87878330–87,893,188 | 21.56 | 13.36 | −0.69 | 0.01 |
TMCO3 | 12:90698789–90,720,756 | 44.09 | 27.02 | −0.71 | 0.01 |
EEF1A1 | 9:13230571–13,237,071 | 210.35 | 128.79 | −0.71 | 0.04 |
RGCC | 12:11625777–11,641,054 | 27.50 | 16.64 | −0.72 | 0.01 |
MAOA | X:105380190–105,462,564 | 9.07 | 5.47 | −0.73 | 0.02 |
ARID5B | 28:18003670–18,195,880 | 12.92 | 7.75 | −0.74 | 0.01 |
SDC4 | 13:74391486–74,412,899 | 35.88 | 21.36 | −0.75 | 0.01 |
CISH | 22:50320204–50,325,618 | 11.74 | 6.97 | −0.75 | 0.01 |
PDE4D | 20:18748597–20,326,423 | 52.28 | 30.49 | −0.78 | 0.01 |
ADAMTS20 | 5:37102284–37,333,841 | 4.75 | 2.75 | −0.79 | 0.01 |
HSPH1 | 12:29820753–29,844,227 | 12.76 | 7.39 | −0.79 | 0.01 |
KIAA1671 | 17:67368397–67,541,098 | 8.79 | 5.08 | −0.79 | 0.01 |
CD160 | 3:21711758–21,725,178 | 3.40 | 1.88 | −0.85 | 0.01 |
SRXN1 | 13:60944182–60,951,049 | 9.83 | 5.29 | −0.89 | 0.01 |
LOC513548 | 9:88273884–88,299,107 | 9.26 | 4.94 | −0.91 | 0.01 |
KLHL30 | 3:118105157–118,112,080 | 17.70 | 9.10 | −0.96 | 0.01 |
TNFRSF12A | 25:2435179–2,441,777 | 64.37 | 32.72 | −0.98 | 0.01 |
CDKN1A | 23:10551754–10,568,782 | 27.80 | 13.85 | −1.01 | 0.01 |
MYBPH | 16:760047–769,469 | 79.15 | 39.33 | −1.01 | 0.02 |
SMPDL3A | 9:28811575–28,829,543 | 11.21 | 5.53 | −1.02 | 0.01 |
LOC104971692 | 3:66997750–67,054,450 | 169.28 | 80.23 | −1.08 | 0.01 |
GFPT2 | 7:772036–817,756 | 5.13 | 2.42 | −1.08 | 0.01 |
GNPTAB | 5:65912911–65,996,254 | 13.49 | 6.24 | −1.11 | 0.01 |
SPOCK2 | 28:28304693–28,329,944 | 6.10 | 2.82 | −1.11 | 0.01 |
MICAL2 | 15:40914779–41,195,753 | 21.93 | 9.98 | −1.14 | 0.01 |
RNF115 | 3:21626658–21,706,296 | 86.33 | 39.05 | −1.14 | 0.01 |
LOC781186 | 20:3132654–3,195,037 | 34.42 | 15.42 | −1.16 | 0.02 |
IL1RAP | 1:77187089–77,343,695 | 2.36 | 1.04 | −1.18 | 0.01 |
RGS2 | 16:13041891–13,045,246 | 14.64 | 6.41 | −1.19 | 0.01 |