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Table 3 MiRNA-like molecules identified using structural search and ab initio prediction

From: Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma

Candidate number

Ext

Chr

Start Position

End Position

Pred

Length

SnoReport score

HMMiR likelihood ratio

Fold-change (N0/N+)

356

Both

chr4

102,540,761

102,541,036

miRNA

276

0

0.69

13.58

1731

Both

chr4

112,606,383

112,606,658

miRNA

276

0

0.7

56.18

1731

5'

chr4

112,606,478

112,606,658

miRNA

181

0

0.7

56.18

6039

Both

chr3

155,125,921

155,126,196

snoRNA C/D

276

0.99 (−)

0

48.87

6039

3'

chr3

155,125,921

155,126,101

snoRNA

C/D

181

0.99 (−)

0

48.87

8442

Both

chr21

19,709,655

19,709,930

snoRNA

C/D

276

0.99 (−)

0

9.21

12,375

5'

chr19

35,649,281

35,649,461

miRNA

181

0

0.7

12.57

15,215

3'

chr17

51,543,077

51,543,257

miRNA

181

0

0.67

12.94

16,666

Both

chr3

608,518

608,793

snoRNA C/D

276

0.96 (+)

0

−16.14

16,666

3'

chr3

608,518

608,698

snoRNA C/D

181

0.96 (+)

0

−16.14

19,713

Both

chr3

7,941,925

7,942,200

miRNA

276

0

0.69

−21.66

19,713

5'

chr3

7,942,020

7,942,200

miRNA

181

0

0.69

−21.66

  1. Candidate number indicates the number of the read in our dataset. Extension (Ext) indicates which of the three genomic extractions the classification refers to the location of the 120 nucleotide extension performed on the original read (3’- 25 nt upstream, 120 nt downstream, 5’ – 120 nt usptream, 25 nt downstream, Both – 120 nt upstream, 120 nt downstream). Prediction (Pred) indicates the annotation attibuted to the candidate. Positive Fold Change: higher expression in non-metastasized OSCC; negative Fold Change: higher expression in metastasized OSCC