Background
Materials and methods
RNA extraction and fragmentation
Age | Gender | AFP (ng/mg) | Stage (BCLC) | Tumor size (cm) | Tumor metastasis | HBsAG | HBcAb |
---|---|---|---|---|---|---|---|
47 | Male | 2.19 | A1 | 7*5.5*4 | Right lobe of liver | – | + |
45 | Male | 614.1 | A1 | 3.8*3.3*2.7 | No | + | + |
60 | Male | 4602 | A2 | 6*5.3*3.5 | No | + | + |
49 | Male | 191.7 | A1 | 3.5*2.5*2 | No | + | + |
78 | Male | 2.83 | A3 | 4.5*4*2 | No | + | + |
45 | Male | 1.69 | A2 | 2.5*2*2 | No | + | + |
Library construction and sequencing
Identification and analysis of 5-methylcytosine peaks
Patient ID | Sample | Q30 | Sample | Q30 |
---|---|---|---|---|
1 | HCC IP | 92.39% | HCC input | 92.91% |
2 | HCC IP | 92.86% | HCC input | 94.25% |
3 | HCC IP | 93.04% | HCC input | 94.49% |
4 | HCC IP | 93.28% | HCC input | 94.03% |
5 | HCC IP | 93.26% | HCC input | 91.90% |
6 | HCC IP | 92.17% | HCC input | 94.04% |
1 | Paired non-tumor IP | 91.86% | Paired non-tumor input | 93.04% |
2 | Paired non-tumor IP | 91.77% | Paired non-tumor input | 92.96% |
3 | Paired non-tumor IP | 91.55% | Paired non-tumor input | 93.81% |
4 | Paired non-tumor IP | 90.36% | Paired non-tumor input | 94.10% |
5 | Paired non-tumor IP | 91.16% | Paired non-tumor input | 89.47% |
6 | Paired non-tumor IP | 90.86% | paired non-tumor input | 92.47% |
Statistical analysis
Transcriptome sequencing analysis
Bioinformatics analysis
Results
General features of 5-methylcytosine methylation in human HCC and adjacent tissues
Cluster analysis
Chromosome | TxStart | TxEnd | Gene name | Fold change |
---|---|---|---|---|
17 | 44,802,641 | 44,803,000 | GJC1 | 166.3 |
20 | 20,368,103 | 20,368,560 | INSM1 | 107.8 |
8 | 87,871,361 | 87,871,880 | DCAF4L2 | 105.5 |
1 | 27,395,481 | 27,395,814 | GPR3 | 53.6 |
8 | 2,001,041 | 2,001,420 | KBTBD11 | 49.958333 |
6 | 130,438,081 | 130,438,480 | TMEM200A | 46.512195 |
11 | 109,427,881 | 109,428,300 | C11orf87 | 41.321429 |
1 | 14,924,221 | 14,924,540 | KAZN | 40.7 |
X | 37,728,401 | 37,728,740 | XK | 39.196721 |
9 | 16,416,641 | 16,417,340 | BNC2 | 38.307692 |
Chromosome | TxStart | TxEnd | Gene name | Fold change |
---|---|---|---|---|
11 | 75,083,541 | 75,084,020 | OR2AT4 | 139.3 |
11 | 48,325,401 | 48,325,840 | OR4C3 | 134.4 |
10 | 17,137,441 | 17,137,840 | TRDMT1 | 123.9 |
11 | 4,490,301 | 4,490,760 | OR52K1 | 113.9 |
11 | 102,713,021 | 102,713,457 | MMP8 | 109.1 |
8 | 53,225,801 | 53,226,240 | OPRK1 | 108.9 |
14 | 62,109,501 | 62,109,960 | SYT16 | 101.4 |
X | 50,367,561 | 50,368,020 | DGKK | 93.3 |
11 | 5,069,601 | 5,070,240 | OR52E1 | 92.6 |
Y | 5,740,441 | 5,740,880 | PCDH11Y | 92.5 |