Table. 2.
(a) The frequency of deregulated sRNAs in all 35 CRCs based on T/N ratio fingerprint. Gene ratios of each tumor pair (T/N) were calculated and sorted from high to low. Three top upregulated genes and 3 top downregulated genes were selected from each tumor to build tumor fingerprints. The actual ratios of each gene were shown in Table. S3a. (b) Frequency of deregulated sRNAs in 35 CRCs based on subtractive (T-N) RPKM fingerprint. The differences of each tumor pair (T-N) were calculated and sorted from high to low. Three top upregulated and downregulated genes were selected from each tumors and actual differential RPKM were shown in Table. S3b. Commonly deregulated genes presented in more than once in 35 CRCs while uniquely deregulated genes just presented only once in 35 CRCs. (c) Classification of CRCs based on the presence of MT-tRNAs in top 3 upregulated genes according to both ratio and subtractive fingerprints.
| Table. 2a Frequency of sRNAs/miRNA in 3 top up/downregulated genes in T/N ratio fingerprint | |||
|---|---|---|---|
| 13 top upregulated genes in 35 CRCs (T/N: 1.2 to 20X folds) | Total: 105/35 | 14 top downregulated genes in 35 CRCs (N/T: 1.4 to 50X folds) | Total :105/35 |
| MT-tRNA family | 45/35 | snord113-114-116 cluster | 45/35 |
| snord19 cluster | 16/35 | AP000318.1 | 16/15 |
| CTD2651 B20.6 | 13/35 | snord64 | 12/35 |
| snord77 | 8/35 | snord107 | 9/15 |
| snord12 cluster | 7/35 | VTRNA1 | 6/15 |
| snora71D | 6/35 | scarna18 | 4/15 |
| snord78 | 4/35 | snord49B | 3/15 |
| snord98 | 1/35 | snord123 | 3/15 |
| snord49A | 1/35 | mir3607 | 2/15 |
| snord15A | 1/35 | snord71 | 1/15 |
| RNY4 | 1/35 | snord125 | 1/15 |
| snord101 | 1/15 | snord93 | 1/15 |
| snord1A | 1/35 | snord65 | 1/35 |
| snord28 | 1/35 | ||
| Table. 2b Frequency of sRNAs in 3 top up/downregulated genes in T-N subtractive RPKM fingerprint | ||
|---|---|---|
| 5 upregulated sRNAs (T-N=0.5 to 15 × 106 RPKM) | T/N ratio profile | Frequency (total: 105/35) |
| snord12 cluster | 1.5-4 fold | 71/35 |
| snord43 | 1.5-2 folds | 16/35 |
| MT-tRNAs | 1.5-10 folds | 16/35 |
| snord19.2 | 3 fold | 1/35 |
| snord78 | 2 fold | 1/35 |
| 5 downregulated sRNAs (N-T=0.2 to 2 × 106 RPKM) | T/N ratio profile | Frequency (total: 105/35) |
|---|---|---|
| snord71 | 1.5-4 folds | 33/35 |
| snord59A | 1.5-2 folds | 33/35 |
| snord114 cluster | 1.5-4 folds | 20/35 |
| AP0000318.1 | 1.5-4 folds | 18/35 |
| snord107 | 1.5-4 folds | 1/35 |
| Table. 2c CRC subtypes based on both ratio and subtractive fingerprints | |
|---|---|
| Type I | Type II |
| snoRNAs only | MT-tRNAs + snoRNAs |
| T5, T16, T19, T20, T22,T27, T30, T31, T35 | T1, T2, T3, T7,T10, T13, T11, T12, T9, T15, T4, T14, T6, T8, T17, T18, T21, T23, T24, T25, T26, T28, T29, T32, T33, T34 |