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Table 3 Small RNA-Seq analysis of NPC FFPE tissue

From: Methods and matrices: approaches to identifying miRNAs for Nasopharyngeal carcinoma

Down-regulated
miRNA MiRDeep (logFC) MiRExpress (logFC) Family NPC ref.
hsa-let-7b-5p,hsa-let-7b −1.23 −1.17 let-7/98/4458/4500 [36, 50, 51]
hsa-miR-100-5p,hsa-mir-100 −1.72 −1.57 miR-99ab/100 [36, 50, 5254]
hsa-miR-1251,hsa-mir-1251 −5.69 −5.44 miR-1251 -
hsa-miR-1269a,hsa-mir-1269a −6.44 - miR-1269/1269b -
hsa-miR-1269b,hsa-mir-1269b −7.73 −6.14 miR-1269/1269b -
hsa-miR-130a-3p,hsa-mir-130a −2.82 −2.72 miR-130 ac/301ab/301b/301b-3p/454/721/4295/3666 [50, 52, 54]
hsa-miR-133a,hsa-mir-133a-1 −3.75 −3.63 miR-133abc -
hsa-miR-133a,hsa-mir-133a-2 −3.75 −3.63 miR-133abc -
hsa-miR-133b,hsa-mir-133b −2.68 −2.74 miR-133abc -
hsa-miR-136-5p,hsa-mir-136 −2.89 −2.77 miR-136 -
hsa-miR-139-5p,hsa-mir-139 −2.08 −2.04 miR-139-5p [50, 52, 54]
hsa-miR-143-3p,hsa-mir-143 −1.64 −1.40 miR-143/1721/4770 [36, 50, 52, 54]
hsa-miR-145-5p,hsa-mir-145 −2.77 −2.86 miR-145 [36]
hsa-miR-152,hsa-mir-152 −1.72 - miR-148ab-3p/152 [50, 52]
hsa-miR-187-3p,hsa-mir-187 −3.15 - miR-187 [52]
hsa-miR-195-3p,hsa-mir-195 −2.37 −3.02 miR-15abc/16/16abc/195/322/424/497/1907 [50]
hsa-miR-195-5p,hsa-mir-195 −3.06 −2.29 miR-15abc/16/16abc/195/322/424/497/1907 [52]
hsa-miR-199a-5p,hsa-mir-199a-1 −2.46 −2.60 miR-199ab-5p [55]
hsa-miR-199a-5p,hsa-mir-199a-2 −2.46 −2.60 miR-199ab-5p [55]
hsa-mir-199b-5p,hsa-miR-199b - −2.10 miR-199ab-5p [52]
hsa-miR-204-5p,hsa-mir-204 −4.68 −4.62 miR-204/204b/211 [52]
hsa-miR-214-3p,hsa-mir-214 −2.79 −2.83 miR-214/761/3619-5p -
hsa-miR-3065-5p,hsa-mir-3065 −3.73 −3.60 miR-545/3065/3065-5p -
hsa-miR-335-5p,hsa-mir-335 −2.71 −2.68 miR-335/335-5p -
hsa-miR-376a-5p,hsa-mir-376a-1 −3.96 −3.75 miR-376abd/376b-3p -
hsa-miR-376b-5p,hsa-mir-376b −3.45 - miR-376abd/376b-3p -
hsa-miR-376c-5p,hsa-mir-376c −3.45 - miR-376c/741-5p -
hsa-miR-4423-5p,hsa-mir-4423 −6.24 −6.51 miR-4423-5p -
hsa-miR-450a-5p,hsa-mir-450a-1 - −2.06 miR-450a/451a -
hsa-miR-450a-5p,hsa-mir-450a-2 - −2.05 miR-450a/451a -
hsa-miR-4792,hsa-mir-4792 −1.53 - miR-4792 -
hsa-miR-488-3p,hsa-mir-488 −4.86 −4.46 miR-488 -
hsa-miR-497-3p,hsa-mir-497 −3.63 - miR-15abc/16/16abc/195/322/424/497/1907 [50, 52]
hsa-miR-497-5p,hsa-mir-497 −2.53 −2.46 miR-15abc/16/16abc/195/322/424/497/1907 [50, 52]
hsa-miR-504,hsa-mir-504 −3.31 - miR-504/4725-5p -
hsa-miR-539-5p,hsa-mir-539 −6.68 - miR-300/381/539-3p -
hsa-miR-542-3p,hsa-mir-542 −2.02 −1.96 miR-542-3p -
hsa-miR-556-3p,hsa-mir-556 −5.18 - miR-556-5p -
hsa-miR-574-3p,hsa-mir-574 −1.32 −1.25 miR-574-3p -
hsa-miR-585,hsa-mir-585 −2.51 - miR-585 -
hsa-miR-874,hsa-mir-874 −1.68 −1.56 miR-874 -
hsa-miR-887,hsa-mir-887 −1.90 −1.99 miR-887 -
hsa-miR-891a,hsa-mir-891a −7.14 −6.86 miR-891a -
Up-regulated
miRNA MiRDeep (logFC) MiRExpress (logFC) Family NPC ref.
hsa-mir-1268a,hsa-miR-1268a - 2.89 miR-1268/1268b -
hsa-mir-1268b,hsa-miR-1268b - 2.59 miR-1268/1268b -
hsa-miR-1303,hsa-mir-1303 1.61 1.62 miR-1303 -
hsa-miR-1304-3p,hsa-mir-1304 1.56 - miR-1304 -
hsa-miR-1305,hsa-mir-1305 2.84 - miR-1305 -
hsa-mir-15b-5p,hsa-miR-15b - 1.09 miR-15abc/16/16abc/195/322/424/497/1907 [52]
hsa-miR-184,hsa-mir-184 4.84 5.22 miR-184 -
hsa-mir-21-3p,hsa-miR-21 - 1.41 miR-21/590-5p -
hsa-mir-27a-3p,hsa-miR-27a - 1.15 miR-27abc/27a-3p -
hsa-miR-205-3p,hsa-mir-205 2.77 2.65 miR-205/205ab [52]
hsa-miR-205-5p,hsa-mir-205 2.87 2.84 miR-205/205ab [52]
hsa-miR-25-5p,hsa-mir-25 2.21 2.15 miR-25/32/92abc/363/363-3p/367 [52]
hsa-miR-4677-3p,hsa-mir-4677 1.52 1.74 miR-4677-3p -
hsa-mir-4791,hsa-miR-4791 - 2.67 miR-3201/4791 -
hsa-mir-548n,hsa-miR-548n - 3.79 miR-548abakhjiwy/548abcd-5p/559 -
hsa-miR-6510-3p,hsa-mir-6510 2.22 - miR-6510-3p -
hsa-miR-92a-3p,hsa-mir-92a-1 1.32 - miR-25/32/92abc/363/363-3p/367 -
hsa-miR-92a-3p,hsa-mir-92a-2 1.28 - miR-25/32/92abc/363/363-3p/367 -
hsa-mir-944,hsa-miR-944 - 1.47 miR-944 -
EBV specific (All up-regulated)
miRNA MiRDeep (logFC) MiRExpress (logFC)  
ebv-miR-BART1-3p,ebv-mir-BART1 4.54 4.55  
ebv-miR-BART1-5p,ebv-mir-BART1 4.37 4.37
ebv-miR-BART10-3p,ebv-mir-BART10 4.43 4.41
ebv-miR-BART10-5p,ebv-mir-BART10 4.24 4.49
ebv-miR-BART12,ebv-mir-BART12 3.52 3.47
ebv-miR-BART13-3p,ebv-mir-BART13 2.64 2.55
ebv-miR-BART13-5p,ebv-mir-BART13 4.29 4.32
ebv-miR-BART14-3p,ebv-mir-BART14 3.63 3.61
ebv-miR-BART14-5p,ebv-mir-BART14 3.78 3.83
ebv-miR-BART15,ebv-mir-BART15 3.70 3.68
ebv-miR-BART16,ebv-mir-BART16 3.52 3.53
ebv-miR-BART17-3p,ebv-mir-BART17 4.45 4.44
ebv-miR-BART17-5p,ebv-mir-BART17 4.81 4.72
ebv-miR-BART18-3p,ebv-mir-BART18 3.73 3.28
ebv-miR-BART18-5p,ebv-mir-BART18 4.44 4.44
ebv-miR-BART19-3p,ebv-mir-BART19 3.51 3.47
ebv-miR-BART19-5p,ebv-mir-BART19 4.58 -
ebv-miR-BART2-5p,ebv-mir-BART2 3.79 3.72
ebv-miR-BART20-3p,ebv-mir-BART20 3.41 3.39
ebv-miR-BART20-5p,ebv-mir-BART20 4.55 4.62
ebv-miR-BART21-3p,ebv-mir-BART21 2.79 2.71
ebv-miR-BART21-5p,ebv-mir-BART21 3.51 3.50
ebv-miR-BART22,ebv-mir-BART22 3.97 3.93
ebv-miR-BART3-3p,ebv-mir-BART3 4.13 3.83
ebv-miR-BART3-5p,ebv-mir-BART3 4.66 4.50
ebv-miR-BART4-3p,ebv-mir-BART4 3.78 3.66
ebv-miR-BART4-5p,ebv-mir-BART4 3.37 3.32
ebv-miR-BART5-3p,ebv-mir-BART5 4.20 3.82
ebv-miR-BART5-5p,ebv-mir-BART5 3.97 3.89
ebv-miR-BART6-3p,ebv-mir-BART6 4.34 4.29
ebv-miR-BART6-5p,ebv-mir-BART6 4.49 4.35
ebv-miR-BART7-3p,ebv-mir-BART7 4.18 4.15
ebv-miR-BART7-5p,ebv-mir-BART7 5.77 5.76
ebv-miR-BART8-3p,ebv-mir-BART8 4.31 4.26
ebv-miR-BART8-5p,ebv-mir-BART8 4.65 4.63
ebv-miR-BART9-3p,ebv-mir-BART9 4.18 4.05
ebv-miR-BART9-5p,ebv-mir-BART9 4.47 4.45   
  1. Five FFPE samples previously analyzed by microarray were submitted for RNA-Seq and analyzed via both miRExpress and miRDeep tools. Significantly dysregulated miRNAs are listed in Table 3.