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Table 3 Cross-comparison of array and high-throughput sequencing data with differential regulated miRNAs from other studies

From: Analysis options for high-throughput sequencing in miRNA expression profiling

miRNA

Regulation of FTC versus FA (fold change)

Citation

Methodology

Samples

HTS (A)

HTS (B)

HTS (C)

DESeq

Reference

hsa-miR-192-5p

Down (0.67)

Down (0.52)

Down (0.50)

Down (0.55)

Up (1.34)

Weber et al., JCEM [28]

Selection of markers: miRNA microarray

Selection 12 FTC & 8 FA

hsa-miR-192-3p

**-

**-

**-

**-

 

hsa-miR-197-5p

**-

**-

**-

**-

Up (1.82)

hsa-miR-197-3p

Up (1.26)

Up (1.50)

Up (1.30)

Up (1.39)

 

Validation: qPCR

Validation 5 FTC & 4 FA

hsa-miR-328

Down (0.67)

Down (0.59)

Down (0.59)

Down (0.62)

Up (1.49)

hsa-miR-346

**-

**-

**-

**-

Up (1.39)

hsa-miR-146b-5p

Up (2.26)

- (1.04)

- (1.06)

- (0.80)

Up (2.8)

Nikiforova et al., JCEM [27]

Selection of markers: qPCR assay (TaqMan human panel with 158 miRNAs)

Selection 9 FTC & 8 FA

hsa-miR-146b-3p

Up (3.14)

**-

Up (1.50)

**-

hsa-miR-155-5p*

- (1.13)

Down (0.56)

Down (0.50)

Down (0.58)

Up (5.5)

hsa-miR-155-3p

**-

**-

**-

**-

hsa-miR-187-5p

**-

**-

**-

**-

Up (33.4)

hsa-miR-187-3p

**-

**-

**-

**-

hsa-miR-221-5p

- (0.99)

**-

- (0.84)

**-

Up (3.6)

Validation: qPCR

Validation 5 FTC & 4 FA

hsa-miR-221-3p

Up (2.01)

Up (3.08)

***Up (1.78)

Up (3.77)

hsa-miR-222-5p

**-

**-

**-

**-

Up (4.5)

hsa-miR-222-3p

Up (1.96)

Up (1.52)

***Up (1.78)

Up (1.77)

hsa-miR-224-5p

Up (2.26)

**-

**-

**-

Up (6.2)

hsa-miR-224-3p

**-

**-

**-

**-

hsa-miR-199b-5p*

Up (1.58)

Up (1.31)

- (1.04)

Up (1.33)

Down (0.026)

Rossing et al., J MolEndocrinol. [29]

Selection of markers: miRNA microarray

Selection and validation 12 FTC & 12 FA

hsa-miR-199b-3p*

Up (1.35)

Up (1.90)

- (1.19)

- (1.20)

Down (0.082)

hsa-miR-144-5p

Down (0.53)

Down (0.31)

Down (0.34)

Down (0.36)

Down (0.14)

Validation: leave one out cross-validation, cell lines

hsa-miR-144-3p

Down (0.47)

Down (0.50)

Down (0.51)

Down (0.43)

  1. *Very high miRNA abundance of one sample causes increase of mean expression in one of the two tumor groups and may affect fold change result.
  2. **Low abundance (median RPM < 10) or no signal detected.
  3. ***miRNAs have the same seed sequence.